8I0U

The cryo-EM structure of human Bact-IV complex

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

  • Deposited: 2023-01-11 Released: 2024-07-31 
  • Deposition Author(s): Zhan, X., Lu, Y., Shi, Y.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Molecular basis for the activation of human spliceosome.

Zhan, X.Lu, Y.Shi, Y.

(2024) Nat Commun 15: 6348-6348

  • DOI: https://doi.org/10.1038/s41467-024-50785-0
  • Primary Citation of Related Structures:  
    8I0P, 8I0R, 8I0S, 8I0T, 8I0U, 8I0V, 8I0W

  • PubMed Abstract: 

    The spliceosome executes pre-mRNA splicing through four sequential stages: assembly, activation, catalysis, and disassembly. Activation of the spliceosome, namely remodeling of the pre-catalytic spliceosome (B complex) into the activated spliceosome (B act complex) and the catalytically activated spliceosome (B * complex), involves major flux of protein components and structural rearrangements. Relying on a splicing inhibitor, we have captured six intermediate states between the B and B * complexes: pre-B act , B act -I, B act -II, B act -III, B act -IV, and post-B act . Their cryo-EM structures, together with an improved structure of the catalytic step I spliceosome (C complex), reveal how the catalytic center matures around the internal stem loop of U6 snRNA, how the branch site approaches 5'-splice site, how the RNA helicase PRP2 rearranges to bind pre-mRNA, and how U2 snRNP undergoes remarkable movement to facilitate activation. We identify a previously unrecognized key role of PRP2 in spliceosome activation. Our study recapitulates a molecular choreography of the human spliceosome during its catalytic activation.


  • Organizational Affiliation

    Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China. zhanxiechao@westlake.edu.cn.


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 40 kDa proteinD [auth E]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1H [auth I]855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1I [auth J]848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RING finger protein 113AJ [auth K]343Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000125352 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinK [auth L]802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2L [auth M]243Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117614 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homologM [auth N]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22N [auth O]420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologO [auth P]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RNA helicase aquariusP [auth Q]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000021776 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1Q [auth R]536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1R [auth S]166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q9Y3C6 (Homo sapiens)
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GTEx:  ENSG00000137168 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1S [auth T]514Homo sapiensMutation(s): 0 
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Find proteins for O43660 (Homo sapiens)
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GTEx:  ENSG00000171566 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2T [auth U]2,752Homo sapiensMutation(s): 0 
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Find proteins for Q9UQ35 (Homo sapiens)
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GTEx:  ENSG00000167978 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologU [auth V]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163510 
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UniProt GroupQ9HCG8
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17V [auth W]579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16W [auth X]1,041Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for O60231 (Homo sapiens)
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GTEx:  ENSG00000204560 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 4X [auth Y]492Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q8WUA2 (Homo sapiens)
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GTEx:  ENSG00000131013 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27Y [auth Z]225Homo sapiensMutation(s): 0 
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Find proteins for O75934 (Homo sapiens)
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GTEx:  ENSG00000116752 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EZ [auth y]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q9UNP9 (Homo sapiens)
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GTEx:  ENSG00000084072 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'AA [auth a],
WA [auth m]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1AB [auth n],
BA [auth b]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2CA [auth c],
UA [auth h]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FDA [auth d],
VA [auth i]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EEA [auth e],
ZA [auth j]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GFA [auth f],
YA [auth k]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3GA [auth g],
XA [auth l]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19HA [auth q],
IA [auth r],
JA [auth s],
KA [auth t]
504Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000110107 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1LA [auth 1]1,304Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115524 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3MA [auth 3]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''NA [auth p]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3OA [auth w]501Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183431 
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UniProt GroupQ12874
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2PA [auth 2]895Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087365 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4QA [auth 4]424Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143368 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5ARA [auth 7]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100410 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5SA [auth 5]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169976 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BWJ5
Sequence Annotations
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'TA [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 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09661
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNA117Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
U6 snRNAE [auth F]107Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
Pre-mRNAF [auth G]220Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
U2 snRNAG [auth H]188Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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BB [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP

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CB [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

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KB [auth K]
LB [auth N]
MB [auth N]
NB [auth N]
OB [auth 7]
KB [auth K],
LB [auth N],
MB [auth N],
NB [auth N],
OB [auth 7],
PB [auth 7],
QB [auth 7]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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DB [auth C]
EB [auth F]
FB [auth F]
GB [auth F]
HB [auth F]
DB [auth C],
EB [auth F],
FB [auth F],
GB [auth F],
HB [auth F],
IB [auth F],
JB [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
Q [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary