5GAN

The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom


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 1.5 of the entry. See complete history


Literature

Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 angstrom resolution.

Nguyen, T.H.Galej, W.P.Bai, X.C.Oubridge, C.Newman, A.J.Scheres, S.H.Nagai, K.

(2016) Nature 530: 298-302

  • DOI: https://doi.org/10.1038/nature16940
  • Primary Citation of Related Structures:  
    5GAM, 5GAN, 5GAO, 5GAP

  • PubMed Abstract: 

    U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8C [auth A]2,413Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP4D [auth H]465Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 6E [auth J]899Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosomal protein DIB1F [auth D]143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 31G [auth F]494Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP3H [auth G]469Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing helicase BRR2I [auth B]2,163Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown proteinJ [auth x]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BK [auth k],
S [auth b]
196Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1L [auth l],
X [auth h]
146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2M [auth m],
Y [auth j]
110Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3N [auth n],
W [auth d]
101Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EO [auth p],
T [auth e]
94Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FP [auth q],
U [auth f]
86Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GQ [auth r],
V [auth g]
77Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Snu66R [auth E]328Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinAA [auth K]126Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2BA [auth 2]95Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3CA [auth 3]89Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4DA [auth 4]187Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5EA [auth 5]93Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6FA [auth 6]86Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7GA [auth 7]115Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8HA [auth 8]109Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114IA [auth C]1,008Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
U4 snRNAA [auth V]160Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChains LengthOrganismImage
U6 snRNAB [auth W]112Saccharomyces cerevisiae
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Entity ID: 19
MoleculeChains LengthOrganismImage
U5 snRNAZ [auth U]214Saccharomyces cerevisiae
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
JA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Advisory, Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2018-03-21
    Changes: Other, Structure summary
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Other
  • Version 1.5: 2024-05-15
    Changes: Data collection, Database references, Refinement description