9GGR | pdb_00009ggr

Structure of the HrpA-bound E. coli disome, Class II

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The RNA helicase HrpA rescues collided ribosomes in E. coli.

Campbell, A., Esser, H.F., Burroughs, A.M., Berninghausen, O., Aravind, L., Becker, T., Green, R., Beckmann, R., Buskirk, A.R.

(2025) Mol Cell 85: 999-1007.e7

  • DOI: https://doi.org/10.1016/j.molcel.2025.01.018
  • Primary Citation of Related Structures:  
    9GFT, 9GGR

  • PubMed Abstract: 

    Although many antibiotics inhibit bacterial ribosomes, the loss of known factors that rescue stalled ribosomes does not lead to robust antibiotic sensitivity in E. coli, suggesting the existence of additional mechanisms. Here, we show that the RNA helicase HrpA rescues stalled ribosomes in E. coli. Acting selectively on ribosomes that have collided, HrpA uses ATP hydrolysis to split stalled ribosomes into subunits. Cryoelectron microscopy (cryo-EM) structures reveal how HrpA simultaneously binds to two collided ribosomes, explaining its selectivity, and how its helicase module engages downstream mRNA such that, by exerting a pulling force on the mRNA, it would destabilize the stalled ribosome. These studies show that ribosome splitting is a conserved mechanism that allows proteobacteria to tolerate ribosome-targeting antibiotics.

    • Organizational Affiliation: 

    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.


Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2B [auth 1],
P [auth AB]		241Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Explore P0A7V0 
Go to UniProtKB:  P0A7V0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7V0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3C [auth 2],
Q [auth AC]		233Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Explore P0A7V3 
Go to UniProtKB:  P0A7V3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7V3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4D [auth 3],
R [auth AD]		206Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Explore P0A7V8 
Go to UniProtKB:  P0A7V8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7V8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5E [auth 4],
S [auth AE]		167Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Explore P0A7W1 
Go to UniProtKB:  P0A7W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7W1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6, fully modified isoformF [auth 5],
T [auth AF]		135Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02358 (Escherichia coli (strain K12))
Explore P02358 
Go to UniProtKB:  P02358
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02358
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7G [auth 6],
U [auth AG]		179Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02359 (Escherichia coli (strain K12))
Explore P02359 
Go to UniProtKB:  P02359
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02359
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8H [auth 7],
V [auth AH]		130Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Explore P0A7W7 
Go to UniProtKB:  P0A7W7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7W7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9I [auth 8],
W [auth AI]		130Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Explore P0A7X3 
Go to UniProtKB:  P0A7X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7X3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10J [auth 9],
X [auth AJ]		103Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Explore P0A7R5 
Go to UniProtKB:  P0A7R5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7R5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21ID [auth v],
L [auth A1]		71Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
Explore P68679 
Go to UniProtKB:  P68679
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68679
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase HrpAM [auth A2]1,300Escherichia coliMutation(s): 0 
Gene Names: hrpA, b1413, JW5905
EC: 3.6.4.13
UniProt
Find proteins for P43329 (Escherichia coli (strain K12))
Explore P43329 
Go to UniProtKB:  P43329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43329
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL1PB [auth C],
Y [auth AK]		234Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Explore P0A7L0 
Go to UniProtKB:  P0A7L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7L0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13SB [auth F],
Z [auth AL]		118Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Explore P0A7S9 
Go to UniProtKB:  P0A7S9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7S9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14AA [auth AM],
TB [auth G]		101Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG59 (Escherichia coli (strain K12))
Explore P0AG59 
Go to UniProtKB:  P0AG59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG59
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15BA [auth AN],
UB [auth H]		89Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Explore P0ADZ4 
Go to UniProtKB:  P0ADZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADZ4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16CA [auth AO],
VB [auth I]		82Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Explore P0A7T3 
Go to UniProtKB:  P0A7T3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7T3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17DA [auth AP],
WB [auth J]		84Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12))
Explore P0AG63 
Go to UniProtKB:  P0AG63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG63
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18EA [auth AQ],
XB [auth K]		75Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Explore P0A7T7 
Go to UniProtKB:  P0A7T7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7T7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19FA [auth AR],
GD [auth t]		92Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Explore P0A7U3 
Go to UniProtKB:  P0A7U3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7U3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20GA [auth AS],
HD [auth u]		87Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Explore P0A7U7 
Go to UniProtKB:  P0A7U7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7U7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31AHA [auth AT],
YB [auth L]		70Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Explore P0A7M9 
Go to UniProtKB:  P0A7M9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7M9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2CC [auth P],
LA [auth AX]		273Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60422 (Escherichia coli (strain K12))
Explore P60422 
Go to UniProtKB:  P60422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60422
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3DC [auth Q],
MA [auth AY]		209Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
Explore P60438 
Go to UniProtKB:  P60438
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60438
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4EC [auth R],
NA [auth AZ]		201Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
Explore P60723 
Go to UniProtKB:  P60723
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60723
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5FC [auth S],
OA [auth Aa]		179Escherichia coliMutation(s): 0 
UniProt
Find proteins for P62399 (Escherichia coli (strain K12))
Explore P62399 
Go to UniProtKB:  P62399
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62399
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6GC [auth T],
PA [auth Ab]		177Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12))
Explore P0AG55 
Go to UniProtKB:  P0AG55
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG55
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9HC [auth U],
QA [auth Ac]		149Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Explore P0A7R1 
Go to UniProtKB:  P0A7R1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7R1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11IC [auth V],
RA [auth Ad]		142Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Explore P0A7J7 
Go to UniProtKB:  P0A7J7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7J7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13JC [auth W],
SA [auth Ae]		142Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12))
Explore P0AA10 
Go to UniProtKB:  P0AA10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AA10
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14KC [auth X],
TA [auth Af]		123Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Explore P0ADY3 
Go to UniProtKB:  P0ADY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADY3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15LC [auth Y],
UA [auth Ag]		144Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02413 (Escherichia coli (strain K12))
Explore P02413 
Go to UniProtKB:  P02413
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02413
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16MC [auth Z],
VA [auth Ah]		136Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Explore P0ADY7 
Go to UniProtKB:  P0ADY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17NC [auth a],
WA [auth Ai]		127Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12))
Explore P0AG44 
Go to UniProtKB:  P0AG44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG44
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18OC [auth b],
XA [auth Aj]		117Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12))
Explore P0C018 
Go to UniProtKB:  P0C018
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C018
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19PC [auth c],
YA [auth Ak]		115Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Explore P0A7K6 
Go to UniProtKB:  P0A7K6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7K6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20QC [auth d],
ZA [auth Al]		118Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Explore P0A7L3 
Go to UniProtKB:  P0A7L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7L3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21AB [auth Am],
RC [auth e]		103Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
Explore P0AG48 
Go to UniProtKB:  P0AG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG48
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22BB [auth An],
SC [auth f]		110Escherichia coliMutation(s): 0 
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
Explore P61175 
Go to UniProtKB:  P61175
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61175
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23CB [auth Ao],
TC [auth g]		100Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Explore P0ADZ0 
Go to UniProtKB:  P0ADZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADZ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24DB [auth Ap],
UC [auth h]		104Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
Explore P60624 
Go to UniProtKB:  P60624
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60624
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25EB [auth Aq],
VC [auth i]		94Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
Explore P68919 
Go to UniProtKB:  P68919
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68919
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27FB [auth Ar],
WC [auth j]		85Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Explore P0A7L8 
Go to UniProtKB:  P0A7L8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7L8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28GB [auth As],
XC [auth k]		78Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Explore P0A7M2 
Go to UniProtKB:  P0A7M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7M2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29HB [auth At],
YC [auth l]		63Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Explore P0A7M6 
Go to UniProtKB:  P0A7M6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7M6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30IB [auth Au],
ZC [auth m]		59Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
Explore P0AG51 
Go to UniProtKB:  P0AG51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG51
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32AD [auth n],
JB [auth Av]		57Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Explore P0A7N4 
Go to UniProtKB:  P0A7N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7N4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33BD [auth o],
KB [auth Aw]		55Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Explore P0A7N9 
Go to UniProtKB:  P0A7N9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7N9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34CD [auth p],
LB [auth Ax]		46Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Explore P0A7P5 
Go to UniProtKB:  P0A7P5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7P5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35DD [auth q],
MB [auth Ay]		65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Explore P0A7Q1 
Go to UniProtKB:  P0A7Q1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Q1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36AED [auth r],
NB [auth Az]		38Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Explore P0A7Q6 
Go to UniProtKB:  P0A7Q6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Q6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase HrpAOB [auth B]1,326Escherichia coliMutation(s): 0 
Gene Names: hrpA, b1413, JW5905
EC: 3.6.4.13
UniProt
Find proteins for P43329 (Escherichia coli (strain K12))
Explore P43329 
Go to UniProtKB:  P43329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43329
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11LD [auth y],
QB [auth D]		129Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Explore P0A7R9 
Go to UniProtKB:  P0A7R9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7R9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12MD [auth z],
RB [auth E]		124Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Explore P0A7S3 
Go to UniProtKB:  P0A7S3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7S3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
VemP nascent chainFD [auth s]179Vibrio alginolyticusMutation(s): 0 
UniProt
Find proteins for A0A2I3CPK5 (Vibrio alginolyticus (strain ATCC 17749 / DSM 2171 / NBRC 15630 / NCIMB 1903 / NCTC 12160 / XII-53))
Explore A0A2I3CPK5 
Go to UniProtKB:  A0A2I3CPK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2I3CPK5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL10KD [auth x]165Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Explore P0A7J3 
Go to UniProtKB:  P0A7J3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7J3
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth 0],
O [auth AA]		1,542Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains LengthOrganismImage
A-site tRNAK [auth A]76Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains LengthOrganismImage
A-site tRNAN [auth A3]77Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains LengthOrganismImage
P-site tRNAIA [auth AU]76Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains LengthOrganismImage
23S ribosomal RNAAC [auth N],
JA [auth AV]		2,903Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains LengthOrganismImage
5S ribosomal RNABC [auth O],
KA [auth AW]		120Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 60
MoleculeChains LengthOrganismImage
P-site tRNAZB [auth M]75Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 62
MoleculeChains LengthOrganismImage
messenger RNAJD [auth w]57Vibrio alginolyticus
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-19
    Changes: Data collection, Database references