5YZG | pdb_00005yzg

The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom resolution

  • Classification: SPLICING
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2017-12-14 Released: 2018-08-08 
  • Deposition Author(s): Zhan, X., Yan, C., Zhang, X., Lei, J., Shi, Y.
  • Funding Organization(s): Ministry of Science and Technology (China), National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Structure of a human catalytic step I spliceosome

Zhan, X., Yan, C., Zhang, X., Lei, J., Shi, Y.

(2018) Science 359: 537-545

  • DOI: https://doi.org/10.1126/science.aar6401
  • Primary Citation of Related Structures:  
    5YZG

  • PubMed Abstract: 

    Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron microscopy structure of the human C complex at an average resolution of 4.1 angstroms. Compared with the Saccharomyces cerevisiae C complex, the human complex contains 11 additional proteins. The step I splicing factors CCDC49 and CCDC94 (Cwc25 and Yju2 in S. cerevisiae , respectively) closely interact with the DEAH-family adenosine triphosphatase/helicase Prp16 and bridge the gap between Prp16 and the active-site RNA elements. These features, together with structural comparison of the human C and C* complexes, provide mechanistic insights into ribonucleoprotein remodeling and allow the proposition of a working mechanism for the C-to-C* transition.

    • Organizational Affiliation: 
    • Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 82,335Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P2Q9 (Homo sapiens)
Explore Q6P2Q9 
Go to UniProtKB:  Q6P2Q9
PHAROS:  Q6P2Q9
GTEx:  ENSG00000174231 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P2Q9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein component972Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15029 (Homo sapiens)
Explore Q15029 
Go to UniProtKB:  Q15029
PHAROS:  Q15029
GTEx:  ENSG00000108883 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15029
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicase2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O75643 (Homo sapiens)
Explore O75643 
Go to UniProtKB:  O75643
PHAROS:  O75643
GTEx:  ENSG00000144028 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75643
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa protein357Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DI7 (Homo sapiens)
Explore Q96DI7 
Go to UniProtKB:  Q96DI7
PHAROS:  Q96DI7
GTEx:  ENSG00000060688 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96DI7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1855Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCS7 (Homo sapiens)
Explore Q9HCS7 
Go to UniProtKB:  Q9HCS7
PHAROS:  Q9HCS7
GTEx:  ENSG00000076924 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HCS7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1848Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZJ0 (Homo sapiens)
Explore Q9BZJ0 
Go to UniProtKB:  Q9BZJ0
PHAROS:  Q9BZJ0
GTEx:  ENSG00000101343 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZJ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27225Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75934 (Homo sapiens)
Explore O75934 
Go to UniProtKB:  O75934
PHAROS:  O75934
GTEx:  ENSG00000116752 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75934
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like protein802Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99459 (Homo sapiens)
Explore Q99459 
Go to UniProtKB:  Q99459
PHAROS:  Q99459
GTEx:  ENSG00000096401 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99459
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homologM [auth y]307Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULR0 (Homo sapiens)
Explore Q9ULR0 
Go to UniProtKB:  Q9ULR0
GTEx:  ENSG00000240682 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULR0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2N [auth M]243Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O95926 (Homo sapiens)
Explore O95926 
Go to UniProtKB:  O95926
PHAROS:  O95926
GTEx:  ENSG00000117614 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95926
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homologO [auth N]144Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P41223 (Homo sapiens)
Explore P41223 
Go to UniProtKB:  P41223
PHAROS:  P41223
GTEx:  ENSG00000106245 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41223
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22P [auth O]420Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NW64 (Homo sapiens)
Explore Q9NW64 
Go to UniProtKB:  Q9NW64
PHAROS:  Q9NW64
GTEx:  ENSG00000086589 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NW64
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologQ [auth P]229Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P013 (Homo sapiens)
Explore Q9P013 
Go to UniProtKB:  Q9P013
PHAROS:  Q9P013
GTEx:  ENSG00000150316 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P013
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1536Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13573 (Homo sapiens)
Explore Q13573 
Go to UniProtKB:  Q13573
PHAROS:  Q13573
GTEx:  ENSG00000100603 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13573
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3C6 (Homo sapiens)
Explore Q9Y3C6 
Go to UniProtKB:  Q9Y3C6
PHAROS:  Q9Y3C6
GTEx:  ENSG00000137168 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3C6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1514Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O43660 (Homo sapiens)
Explore O43660 
Go to UniProtKB:  O43660
PHAROS:  O43660
GTEx:  ENSG00000171566 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43660
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquariusU [auth Q]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O60306 (Homo sapiens)
Explore O60306 
Go to UniProtKB:  O60306
PHAROS:  O60306
GTEx:  ENSG00000021776 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60306
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2V [auth U]2,752Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQ35 (Homo sapiens)
Explore Q9UQ35 
Go to UniProtKB:  Q9UQ35
PHAROS:  Q9UQ35
GTEx:  ENSG00000167978 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQ35
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologW [auth V]908Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCG8 (Homo sapiens)
Explore Q9HCG8 
Go to UniProtKB:  Q9HCG8
PHAROS:  Q9HCG8
GTEx:  ENSG00000163510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HCG8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17X [auth W]579Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60508 (Homo sapiens)
Explore O60508 
Go to UniProtKB:  O60508
PHAROS:  O60508
GTEx:  ENSG00000168438 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60508
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC25 homologY [auth X]425Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXE8 (Homo sapiens)
Explore Q9NXE8 
Go to UniProtKB:  Q9NXE8
PHAROS:  Q9NXE8
GTEx:  ENSG00000273559 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXE8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 94Z [auth Y]323Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW85 (Homo sapiens)
Explore Q9BW85 
Go to UniProtKB:  Q9BW85
PHAROS:  Q9BW85
GTEx:  ENSG00000105248 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BW85
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16AA [auth Z]1,227Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q92620 (Homo sapiens)
Explore Q92620 
Go to UniProtKB:  Q92620
PHAROS:  Q92620
GTEx:  ENSG00000140829 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92620
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19BA [auth q],
CA [auth r],
DA [auth s],
EA [auth t]		504Homo sapiensMutation(s): 0 
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMS4 (Homo sapiens)
Explore Q9UMS4 
Go to UniProtKB:  Q9UMS4
PHAROS:  Q9UMS4
GTEx:  ENSG00000110107 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UMS4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIIFA [auth u]411Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P38919 (Homo sapiens)
Explore P38919 
Go to UniProtKB:  P38919
PHAROS:  P38919
GTEx:  ENSG00000141543 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38919
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Protein mago nashi homolog 2GA [auth v]148Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96A72 (Homo sapiens)
Explore Q96A72 
Go to UniProtKB:  Q96A72
PHAROS:  Q96A72
GTEx:  ENSG00000111196 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96A72
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 8AHA [auth w]174Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5S9 (Homo sapiens)
Explore Q9Y5S9 
Go to UniProtKB:  Q9Y5S9
PHAROS:  Q9Y5S9
GTEx:  ENSG00000265241 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5S9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Protein CASC3IA [auth x]703Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O15234 (Homo sapiens)
Explore O15234 
Go to UniProtKB:  O15234
PHAROS:  O15234
GTEx:  ENSG00000108349 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15234
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3JA [auth h],
SA [auth a]		126Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62318 (Homo sapiens)
Explore P62318 
Go to UniProtKB:  P62318
PHAROS:  P62318
GTEx:  ENSG00000100028 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62318
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'KA [auth i],
TA [auth b]		229Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P14678 (Homo sapiens)
Explore P14678 
Go to UniProtKB:  P14678
PHAROS:  P14678
GTEx:  ENSG00000125835 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14678
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1LA [auth j],
UA [auth c]		119Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62314 (Homo sapiens)
Explore P62314 
Go to UniProtKB:  P62314
PHAROS:  P62314
GTEx:  ENSG00000167088 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62314
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2MA [auth k],
VA [auth d]		118Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62316 (Homo sapiens)
Explore P62316 
Go to UniProtKB:  P62316
PHAROS:  P62316
GTEx:  ENSG00000125743 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62316
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FNA [auth m],
WA [auth f]		86Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62306 (Homo sapiens)
Explore P62306 
Go to UniProtKB:  P62306
PHAROS:  P62306
GTEx:  ENSG00000139343 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62306
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EOA [auth l],
XA [auth e]		92Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62304 (Homo sapiens)
Explore P62304 
Go to UniProtKB:  P62304
PHAROS:  P62304
GTEx:  ENSG00000182004 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62304
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GPA [auth n],
YA [auth g]		76Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62308 (Homo sapiens)
Explore P62308 
Go to UniProtKB:  P62308
PHAROS:  P62308
GTEx:  ENSG00000143977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62308
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'QA [auth o]255Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P09661 (Homo sapiens)
Explore P09661 
Go to UniProtKB:  P09661
GTEx:  ENSG00000131876 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09661
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''RA [auth p]225Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P08579 (Homo sapiens)
Explore P08579 
Go to UniProtKB:  P08579
PHAROS:  P08579
GTEx:  ENSG00000125870 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08579
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EZA [auth 1]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNP9 (Homo sapiens)
Explore Q9UNP9 
Go to UniProtKB:  Q9UNP9
PHAROS:  Q9UNP9
GTEx:  ENSG00000084072 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNP9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidylprolyl isomerase domain and WD repeat-containing protein 1AB [auth 2]646Homo sapiensMutation(s): 0 
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BP3 (Homo sapiens)
Explore Q96BP3 
Go to UniProtKB:  Q96BP3
PHAROS:  Q96BP3
GTEx:  ENSG00000113593 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96BP3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase GBB [auth 3]754Homo sapiensMutation(s): 0 
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13427 (Homo sapiens)
Explore Q13427 
Go to UniProtKB:  Q13427
PHAROS:  Q13427
GTEx:  ENSG00000138398 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13427
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
UNKNOWCB [auth 4]37Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNA117Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains LengthOrganismImage
U6 snRNA107Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains LengthOrganismImage
Pre-mRNA275Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains LengthOrganismImage
U2 snRNA188Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP
Download Ideal Coordinates CCD File 
DB [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP
Download Ideal Coordinates CCD File 
EB [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP
Query on ATP
Download Ideal Coordinates CCD File 
VB [auth u]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP
Download Ideal Coordinates CCD File 
GB [auth D],
HB [auth D]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
NB [auth N]
OB [auth N]
PB [auth N]
QB [auth O]
RB [auth O]
NB [auth N],
OB [auth N],
PB [auth N],
QB [auth O],
RB [auth O],
SB [auth O],
TB [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
FB [auth C]
IB [auth F]
JB [auth F]
KB [auth F]
LB [auth F]
FB [auth C],
IB [auth F],
JB [auth F],
KB [auth F],
LB [auth F],
MB [auth F],
UB [auth u]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
R
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

Structure Validation

View Full Validation Report



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

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2014ZX09507003006
National Natural Science Foundation of ChinaChina31130002
National Natural Science Foundation of ChinaChina31321062

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other
  • Version 2.0: 2020-10-14
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary