8Y7E

Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U12 snRNP part


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.66 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 basis of U12-type intron engagement by the fully assembled human minor spliceosome.

Bai, R.Yuan, M.Zhang, P.Luo, T.Shi, Y.Wan, R.

(2024) Science 383: 1245-1252

  • DOI: https://doi.org/10.1126/science.adn7272
  • Primary Citation of Related Structures:  
    8Y6O, 8Y7E

  • PubMed Abstract: 

    The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we report the 3.3-angstrom cryo-electron microscopy structure of the fully assembled human minor spliceosome pre-B complex. The atomic model includes U11 small nuclear ribonucleoprotein (snRNP), U12 snRNP, and U4atac/U6atac.U5 tri-snRNP. U11 snRNA is recognized by five U11-specific proteins (20K, 25K, 35K, 48K, and 59K) and the heptameric Sm ring. The 3' half of the 5'-splice site forms a duplex with U11 snRNA; the 5' half is recognized by U11-35K, U11-48K, and U11 snRNA. Two proteins, CENATAC and DIM2/TXNL4B, specifically associate with the minor tri-snRNP. A structural analysis uncovered how two conformationally similar tri-snRNPs are differentiated by the minor and major prespliceosomes for assembly.


  • Organizational Affiliation

    Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1B [auth 1]1,304Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115524 
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UniProt GroupO75533
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2C [auth 2]895Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087365 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3D [auth 3]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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UniProt GroupQ15393
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4E [auth 4]424Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143368 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6F [auth 5]125Homo sapiensMutation(s): 0 
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PHAROS:  Q9Y3B4
GTEx:  ENSG00000115128 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AG [auth 6]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100410 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5H [auth 7]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169976 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3J [auth h]126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'K [auth i]240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1L [auth j]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2M [auth k]118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EN [auth l]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FO [auth m]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GP [auth n]76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel modifier 1Q [auth v]230Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163156 
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Entity ID: 1
MoleculeChains LengthOrganismImage
pre-mRNA280Homo sapiens
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Entity ID: 9
MoleculeChains LengthOrganismImage
U12 snRNAI [auth H]150Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.66 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)China32171214
National Natural Science Foundation of China (NSFC)China31930059
National Natural Science Foundation of China (NSFC)China32100987

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references