5YZG

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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 82,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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UniProt GroupQ6P2Q9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein component972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicase2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa protein357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116752 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like protein802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homologM [auth y]307Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000240682 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2N [auth M]243Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117614 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homologO [auth N]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22P [auth O]420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologQ [auth P]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000137168 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquariusU [auth Q]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000021776 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2V [auth U]2,752Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167978 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologW [auth V]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163510 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17X [auth W]579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC25 homologY [auth X]425Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000273559 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 94Z [auth Y]323Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105248 
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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
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GTEx:  ENSG00000140829 
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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
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GTEx:  ENSG00000110107 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIIFA [auth u]411Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000141543 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Protein mago nashi homolog 2GA [auth v]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111196 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 8AHA [auth w]174Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265241 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Protein CASC3IA [auth x]703Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108349 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3JA [auth h],
SA [auth a]		126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'KA [auth i],
TA [auth b]		229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1LA [auth j],
UA [auth c]		119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2MA [auth k],
VA [auth d]		118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FNA [auth m],
WA [auth f]		86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EOA [auth l],
XA [auth e]		92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GPA [auth n],
YA [auth g]		76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'QA [auth o]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''RA [auth p]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EZA [auth 1]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000084072 
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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  
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UniProt GroupQ96BP3
Sequence Annotations
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  • Reference Sequence
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(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
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(by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
UNKNOWCB [auth 4]37Homo sapiensMutation(s): 0 
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  • 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
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EB [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP
Query on ATP
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VB [auth u]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP
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GB [auth D],
HB [auth D]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN
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NB [auth N]
OB [auth N]
PB [auth N]
QB [auth O]
RB [auth O]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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FB [auth C]
IB [auth F]
JB [auth F]
KB [auth F]
LB [auth F]
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

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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