5NRL

Structure of a pre-catalytic spliceosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of a pre-catalytic spliceosome.

Plaschka, C.Lin, P.C.Nagai, K.

(2017) Nature 546: 617-621

  • DOI: 10.1038/nature22799
  • Primary Citation of Related Structures:  
    5NRL

  • PubMed Abstract: 
  • Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae pre-catalytic B complex spliceosome at near-atomic resolution ...

    Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae pre-catalytic B complex spliceosome at near-atomic resolution. The mobile U2 small nuclear ribonucleoprotein particle (snRNP) associates with U4/U6.U5 tri-snRNP through the U2/U6 helix II and an interface between U4/U6 di-snRNP and the U2 snRNP SF3b-containing domain, which also transiently contacts the helicase Brr2. The 3' region of the U2 snRNP is flexibly attached to the SF3b-containing domain and protrudes over the concave surface of tri-snRNP, where the U1 snRNP may reside before its release from the pre-mRNA 5' splice site. The U6 ACAGAGA sequence forms a hairpin that weakly tethers the 5' splice site. The B complex proteins Prp38, Snu23 and Spp381 bind the Prp8 N-terminal domain and stabilize U6 ACAGAGA stem-pre-mRNA and Brr2-U4 small nuclear RNA interactions. These results provide important insights into the events leading to active site formation.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3 389Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7 7115Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8 8109Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8 A2413Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing helicase BRR2 B2163Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114 C1008Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosomal protein DIB1 D143Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
66 kDa U4/U6.U5 small nuclear ribonucleoprotein component E587Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 31 F494Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP3 G469Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP4 H465Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 6 J899Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated protein K126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
23 kDa U4/U6.U5 small nuclear ribonucleoprotein component L194Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38 M242Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPP381 N291Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
U2 snRNP component HSH155 O971Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RSE1 P1361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Cold sensitive U2 snRNA suppressor 1 Q435Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Protein HSH49 R213Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q99181 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RDS3 S107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP9 T530Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP11 U266Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
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Pre-mRNA-splicing factor PRP21 V280Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A' W238Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown X111Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
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U2 small nuclear ribonucleoprotein B'' Y111Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
RDS3 complex subunit 10 Z85Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
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U6 snRNA-associated Sm-like protein LSm2 a95Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein B bks196Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 dnv101Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E epw94Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F fqx86Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
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Small nuclear ribonucleoprotein G gry77Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1 hlt146Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
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Small nuclear ribonucleoprotein Sm D2 imu110Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
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U6 snRNA-associated Sm-like protein LSm4 j187Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
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U6 snRNA-associated Sm-like protein LSm5 o93Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
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U6 snRNA-associated Sm-like protein LSm6 z86Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for A6ZYX7 (Saccharomyces cerevisiae (strain YJM789))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U2 snRNA21175Saccharomyces cerevisiae
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Entity ID: 3
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U4 snRNA4160Saccharomyces cerevisiae
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Entity ID: 4
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U5 snRNA5214Saccharomyces cerevisiae
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Entity ID: 5
MoleculeChainsLengthOrganismImage
U6 snRNA6112Saccharomyces cerevisiae
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Entity ID: 16
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Yeast UBC4 gene for ubiquitin-conjugating enzymeI95Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184330
European Research CouncilUnited Kingdom693087 - SPLICE3D

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references, Derived calculations
  • Version 1.2: 2017-07-19
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2018-03-21
    Changes: Advisory, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.5: 2018-11-28
    Changes: Advisory, Data collection, Database references, Derived calculations