8H6J

Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into human exon-defined spliceosome prior to activation.

Zhang, W.Zhang, X.Zhan, X.Bai, R.Lei, J.Yan, C.Shi, Y.

(2024) Cell Res 

  • DOI: https://doi.org/10.1038/s41422-024-00949-w
  • Primary Citation of Related Structures:  
    8H6E, 8H6J, 8H6K, 8H6L

  • PubMed Abstract: 

    Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, the structure of a fully assembled exon-defined spliceosome remains at large. During spliceosome assembly, the pre-catalytic state (B complex) is converted from its precursor (pre-B complex). Here we report atomic structures of the exon-defined human spliceosome in four sequential states: mature pre-B, late pre-B, early B, and mature B. In the previously unknown late pre-B state, U1 snRNP is already released but the remaining proteins are still in the pre-B state; unexpectedly, the RNAs are in the B state, with U6 snRNA forming a duplex with 5'-splice site and U5 snRNA recognizing the 3'-end of the exon. In the early and mature B complexes, the B-specific factors are stepwise recruited and specifically recognize the exon 3'-region. Our study reveals key insights into the assembly of the exon-defined spliceosomes and identifies mechanistic steps of the pre-B-to-B transition.


  • Organizational Affiliation

    Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2C [auth 6a]95Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204392 
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UniProt GroupQ9Y333
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3D [auth 6b]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170860 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4E [auth 6c]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130520 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5F [auth 6d]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106355 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6G [auth 6e]80Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164167 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7H [auth 6f]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130332 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8I [auth 6g]96Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128534 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8K [auth 5B]2,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentL [auth 5C]972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseM [auth 5D]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinN [auth 5E]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform SM-B of Small nuclear ribonucleoprotein-associated proteins B and B'CB [auth 2a],
IA [auth 4a],
O [auth 5a]
231Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1DB [auth 2b],
JA [auth 4b],
P [auth 5b]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2EB [auth 2c],
KA [auth 4c],
Q [auth 5c]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FFB [auth 2d],
LA [auth 4d],
R [auth 5d]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EGB [auth 2e],
MA [auth 4e],
S [auth 5e]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GHB [auth 2f],
NA [auth 4f],
T [auth 5f]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3IB [auth 2g],
OA [auth 4g],
U [auth 5g]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp3W [auth 4B]683Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117360 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp4X [auth 4C]522Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136875 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp31Y [auth 4D]499Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105618 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NHP2-like protein 1Z [auth 4E]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100138 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin-like protein 4AAA [auth 4F]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141759 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 6BA [auth 4G]941Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101161 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 42CA [auth 4R]480Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000126254 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 1DA [auth 4S]800Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175467 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 2EA [auth 4T]565Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168883 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX23FA [auth 4U]820Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000174243 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6.U5 small nuclear ribonucleoprotein 27 kDa proteinGA [auth 4X]155Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124380 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PRP4 homologHA [auth 4Y]1,007Homo sapiensMutation(s): 0 
EC: 2.7.11.1
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GTEx:  ENSG00000112739 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'QA [auth 2B]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''RA [auth 2C]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1SA [auth 2D]793Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099995 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2TA [auth 2E]464Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104897 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3UA [auth 2F]501Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183431 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1VA [auth 2G]1,304Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115524 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2WA [auth 2H]895Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087365 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3XA [auth 2I]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4YA [auth 2J]424Homo sapiensMutation(s): 0 
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Find proteins for Q15427 (Homo sapiens)
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PHAROS:  Q15427
GTEx:  ENSG00000143368 
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UniProt GroupQ15427
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6ZA [auth 2K]125Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3B4 (Homo sapiens)
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PHAROS:  Q9Y3B4
GTEx:  ENSG00000115128 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AAB [auth 2L]110Homo sapiensMutation(s): 0 
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Find proteins for Q7RTV0 (Homo sapiens)
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PHAROS:  Q7RTV0
GTEx:  ENSG00000100410 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5BB [auth 2M]86Homo sapiensMutation(s): 0 
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PHAROS:  Q9BWJ5
GTEx:  ENSG00000169976 
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Entity ID: 1
MoleculeChains LengthOrganismImage
pre-mRNA144Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
U6 snRNAB [auth 6A]107Homo sapiens
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Entity ID: 10
MoleculeChains LengthOrganismImage
U5 snRNAJ [auth 5A]117Homo sapiens
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Entity ID: 22
MoleculeChains LengthOrganismImage
U4 snRNAV [auth 4A]144Homo sapiens
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Entity ID: 35
MoleculeChains LengthOrganismImage
U2 snRNAPA [auth 2A]188Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31930059

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references