8QPA

Cryo-EM Structure of Pre-B+5'ssLNG Complex (core part)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

Structural insights into the cross-exon to cross-intron spliceosome switch.

Zhang, Z.Kumar, V.Dybkov, O.Will, C.L.Zhong, J.Ludwig, S.E.J.Urlaub, H.Kastner, B.Stark, H.Luhrmann, R.

(2024) Nature 630: 1012-1019

  • DOI: https://doi.org/10.1038/s41586-024-07458-1
  • Primary Citation of Related Structures:  
    8QOZ, 8QP8, 8QP9, 8QPA, 8QPB, 8QPE, 8QPK, 8QXD, 8QZS, 8R08, 8R09, 8R0A, 8R0B, 8RM5

  • PubMed Abstract: 

    Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron 1 . Alternatively, it can occur through an exon-defined pathway 2-5 , whereby U2 binds the branch site located upstream of the defined exon and U1 snRNP interacts with the 5' splice site located directly downstream of it. The U4/U6.U5 tri-snRNP subsequently binds to produce a cross-intron (CI) or cross-exon (CE) pre-B complex, which is then converted to the spliceosomal B complex 6,7 . Exon definition promotes the splicing of upstream introns 2,8,9 and plays a key part in alternative splicing regulation 10-16 . However, the three-dimensional structure of exon-defined spliceosomal complexes and the molecular mechanism of the conversion from a CE-organized to a CI-organized spliceosome, a pre-requisite for splicing catalysis, remain poorly understood. Here cryo-electron microscopy analyses of human CE pre-B complex and B-like complexes reveal extensive structural similarities with their CI counterparts. The results indicate that the CE and CI spliceosome assembly pathways converge already at the pre-B stage. Add-back experiments using purified CE pre-B complexes, coupled with cryo-electron microscopy, elucidate the order of the extensive remodelling events that accompany the formation of B complexes and B-like complexes. The molecular triggers and roles of B-specific proteins in these rearrangements are also identified. We show that CE pre-B complexes can productively bind in trans to a U1 snRNP-bound 5' splice site. Together, our studies provide new mechanistic insights into the CE to CI switch during spliceosome assembly and its effect on pre-mRNA splice site pairing at this stage.


  • Organizational Affiliation

    Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseA [auth B]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX23B [auth G]820Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000174243 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp3C [auth J]683Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117360 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp31D [auth L]499Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105618 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp4E [auth F]522Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136875 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 6F [auth N]941Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101161 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8G [auth A]2,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 39H [auth U]565Homo sapiensMutation(s): 0 
EC: 3.4.19.12
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GTEx:  ENSG00000168883 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 1I [auth S]800Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175467 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentJ [auth C]972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NHP2-like protein 1, N-terminally processedK [auth M]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100138 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin-like protein 4AL [auth D]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141759 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1O [auth 7]793Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099995 
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Entity ID: 13
MoleculeChains LengthOrganismImage
U5 snRNAM [auth 5]117Homo sapiens
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Entity ID: 14
MoleculeChains LengthOrganismImage
5'ss oligoN [auth z]18Homo sapiens
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Entity ID: 16
MoleculeChains LengthOrganismImage
U4 snRNAP [auth 4]144Homo sapiens
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Entity ID: 17
MoleculeChains LengthOrganismImage
U6 snRNAQ [auth 6]106Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
R [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection, Database references