9B51 | pdb_00009b51

E. coli 70S ribosome complex (N1-methylated 16S A1408 + G418)

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-03-21 Released: 2025-08-27 
  • Deposition Author(s): Mattingly, J.M., Dey, D., Zelinskaya, N., Dunham, C.M., Conn, G.L.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Simons Foundation, National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Basis for selective drug evasion of an aminoglycoside-resistance ribosomal RNA modification

Dey, D., Mattingly, J.M., Zelinskaya, N., Dunham, C.M., Conn, G.L.

(2025) Nat Commun 


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB]240Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC]233Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD]206Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE]167Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF]135Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG]179Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH]130Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth AI]130Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth AJ]103Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth AK]129Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth AL]124Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth AM]118Escherichia coliMutation(s): 0 
UniProt
Find proteins for A0A7U9IV78 (Escherichia coli HVH 36)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth AN]101Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth AO]89Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP]82Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ]84Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth AR]75Escherichia coliMutation(s): 0 
UniProt
Find proteins for A0A0E2KXL3 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth AS]92Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth AT]87Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth AU]71Escherichia coliMutation(s): 0 
UniProt
Find proteins for A0A0E2L2J1 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32Z [auth B0]57Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AA [auth B1]55Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth B2]46Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth B3]65Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth B4]38Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31EA [auth B5]70Escherichia coliMutation(s): 0 
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Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2HA [auth BC]273Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3IA [auth BD]209Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4JA [auth BE]201Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5KA [auth BF]179Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6LA [auth BG]177Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9MA [auth BH]149Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13NA [auth BJ]142Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14OA [auth BK]123Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15PA [auth BL]144Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16QA [auth BM]136Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17RA [auth BN]127Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18SA [auth BO]117Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19TA [auth BP]115Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20UA [auth BQ]118Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21VA [auth BR]103Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22WA [auth BS]110Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23XA [auth BT]100Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24YA [auth BU]104Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25ZA [auth BV]94Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AB [auth BW]85Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BB [auth BX]78Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CB [auth BY]63Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DB [auth BZ]59Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA]1,539Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
mRNAV [auth AV]89Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
tRNA-ValW [auth AW],
Y [auth AY]		76Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
tRNA-fMetX [auth AX]77Escherichia coli
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains LengthOrganismImage
23S ribosomal RNAFA [auth BA]2,903Escherichia coli
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains LengthOrganismImage
5S ribosomal RNAGA [auth BB]120Escherichia coli
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GET (Subject of Investigation/LOI)
Query on GET
Download Ideal Coordinates CCD File 
TE [auth AA],
UE [auth AA]		GENETICIN
C20 H40 N4 O10
BRZYSWJRSDMWLG-DJWUNRQOSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
XE [auth B4],
YE [auth B5]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AC [auth AA]
AD [auth AA]
AE [auth AA]
AF [auth BA]
AG [auth BA]
AC [auth AA],
AD [auth AA],
AE [auth AA],
AF [auth BA],
AG [auth BA],
AH [auth BA],
AI [auth BA],
AJ [auth BA],
AK [auth BA],
AL [auth BA],
AM [auth BA],
AN [auth BB],
BC [auth AA],
BD [auth AA],
BE [auth AA],
BF [auth BA],
BG [auth BA],
BH [auth BA],
BI [auth BA],
BJ [auth BA],
BK [auth BA],
BL [auth BA],
BM [auth BA],
BN [auth BB],
CC [auth AA],
CD [auth AA],
CE [auth AA],
CF [auth BA],
CG [auth BA],
CH [auth BA],
CI [auth BA],
CJ [auth BA],
CK [auth BA],
CL [auth BA],
CM [auth BA],
CN [auth BB],
DC [auth AA],
DD [auth AA],
DE [auth AA],
DF [auth BA],
DG [auth BA],
DH [auth BA],
DI [auth BA],
DJ [auth BA],
DK [auth BA],
DL [auth BA],
DM [auth BA],
DN [auth BB],
EB [auth AA],
EC [auth AA],
ED [auth AA],
EE [auth AA],
EF [auth BA],
EG [auth BA],
EH [auth BA],
EI [auth BA],
EJ [auth BA],
EK [auth BA],
EL [auth BA],
EM [auth BA],
EN [auth BB],
FB [auth AA],
FC [auth AA],
FD [auth AA],
FE [auth AA],
FF [auth BA],
FG [auth BA],
FH [auth BA],
FI [auth BA],
FJ [auth BA],
FK [auth BA],
FL [auth BA],
FM [auth BA],
GB [auth AA],
GC [auth AA],
GD [auth AA],
GE [auth AA],
GF [auth BA],
GG [auth BA],
GH [auth BA],
GI [auth BA],
GJ [auth BA],
GK [auth BA],
GL [auth BA],
GM [auth BA],
HB [auth AA],
HC [auth AA],
HD [auth AA],
HE [auth AA],
HF [auth BA],
HG [auth BA],
HH [auth BA],
HI [auth BA],
HJ [auth BA],
HK [auth BA],
HL [auth BA],
HM [auth BA],
IB [auth AA],
IC [auth AA],
ID [auth AA],
IE [auth AA],
IF [auth BA],
IG [auth BA],
IH [auth BA],
II [auth BA],
IJ [auth BA],
IK [auth BA],
IL [auth BA],
IM [auth BA],
JB [auth AA],
JC [auth AA],
JD [auth AA],
JE [auth AA],
JF [auth BA],
JG [auth BA],
JH [auth BA],
JI [auth BA],
JJ [auth BA],
JK [auth BA],
JL [auth BA],
JM [auth BA],
KB [auth AA],
KC [auth AA],
KD [auth AA],
KE [auth AA],
KF [auth BA],
KG [auth BA],
KH [auth BA],
KI [auth BA],
KJ [auth BA],
KK [auth BA],
KL [auth BA],
KM [auth BA],
LB [auth AA],
LC [auth AA],
LD [auth AA],
LE [auth AA],
LF [auth BA],
LG [auth BA],
LH [auth BA],
LI [auth BA],
LJ [auth BA],
LK [auth BA],
LL [auth BA],
LM [auth BA],
MB [auth AA],
MC [auth AA],
MD [auth AA],
ME [auth AA],
MF [auth BA],
MG [auth BA],
MH [auth BA],
MI [auth BA],
MJ [auth BA],
MK [auth BA],
ML [auth BA],
MM [auth BA],
NB [auth AA],
NC [auth AA],
ND [auth AA],
NE [auth AA],
NF [auth BA],
NG [auth BA],
NH [auth BA],
NI [auth BA],
NJ [auth BA],
NK [auth BA],
NL [auth BA],
NM [auth BA],
OB [auth AA],
OC [auth AA],
OD [auth AA],
OE [auth AA],
OF [auth BA],
OG [auth BA],
OH [auth BA],
OI [auth BA],
OJ [auth BA],
OK [auth BA],
OL [auth BA],
OM [auth BA],
PB [auth AA],
PC [auth AA],
PD [auth AA],
PE [auth AA],
PF [auth BA],
PG [auth BA],
PH [auth BA],
PI [auth BA],
PJ [auth BA],
PK [auth BA],
PL [auth BA],
PM [auth BA],
QB [auth AA],
QC [auth AA],
QD [auth AA],
QE [auth AA],
QF [auth BA],
QG [auth BA],
QH [auth BA],
QI [auth BA],
QJ [auth BA],
QK [auth BA],
QL [auth BA],
QM [auth BA],
RB [auth AA],
RC [auth AA],
RD [auth AA],
RE [auth AA],
RF [auth BA],
RG [auth BA],
RH [auth BA],
RI [auth BA],
RJ [auth BA],
RK [auth BA],
RL [auth BA],
RM [auth BA],
SB [auth AA],
SC [auth AA],
SD [auth AA],
SE [auth AA],
SF [auth BA],
SG [auth BA],
SH [auth BA],
SI [auth BA],
SJ [auth BA],
SK [auth BA],
SL [auth BA],
SM [auth BA],
TB [auth AA],
TC [auth AA],
TD [auth AA],
TF [auth BA],
TG [auth BA],
TH [auth BA],
TI [auth BA],
TJ [auth BA],
TK [auth BA],
TL [auth BA],
TM [auth BA],
UB [auth AA],
UC [auth AA],
UD [auth AA],
UF [auth BA],
UG [auth BA],
UH [auth BA],
UI [auth BA],
UJ [auth BA],
UK [auth BA],
UL [auth BA],
UM [auth BA],
VB [auth AA],
VC [auth AA],
VD [auth AA],
VE [auth B0],
VF [auth BA],
VG [auth BA],
VH [auth BA],
VI [auth BA],
VJ [auth BA],
VK [auth BA],
VL [auth BA],
VM [auth BA],
WB [auth AA],
WC [auth AA],
WD [auth AA],
WE [auth B0],
WF [auth BA],
WG [auth BA],
WH [auth BA],
WI [auth BA],
WJ [auth BA],
WK [auth BA],
WL [auth BA],
WM [auth BA],
XB [auth AA],
XC [auth AA],
XD [auth AA],
XF [auth BA],
XG [auth BA],
XH [auth BA],
XI [auth BA],
XJ [auth BA],
XK [auth BA],
XL [auth BA],
XM [auth BA],
YB [auth AA],
YC [auth AA],
YD [auth AA],
YF [auth BA],
YG [auth BA],
YH [auth BA],
YI [auth BA],
YJ [auth BA],
YK [auth BA],
YL [auth BA],
YM [auth BA],
ZB [auth AA],
ZC [auth AA],
ZD [auth AA],
ZE [auth BA],
ZF [auth BA],
ZG [auth BA],
ZH [auth BA],
ZI [auth BA],
ZJ [auth BA],
ZK [auth BA],
ZL [auth BA],
ZM [auth BA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.20

Structure Validation

View Full Validation Report



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

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI088025
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM135060
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129547
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129539
Simons FoundationUnited StatesSF349247
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesUL1TR000454

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release