5GAN

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 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

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: 10.1038/nature16940
  • Primary Citation of Related Structures:  
  • Also Cited By: 5MQ0, 5MPS

  • 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 p ...

    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.


    Related Citations: 
    • The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
      Nguyen, T.H.D.,Galej, W.,Bai, X.C.,Savva, C.G.,Newman, A.J.,Scheres, S.H.W.,Nagai, K.
      (2015) Nature 523: 47


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
2413Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP8 (DBF3, DNA39, RNA8, SLT21, USA2)
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33334
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP4
H
465Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP4 (RNA4)
Find proteins for P20053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20053
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 6
J
899Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP6 (RNA6)
Find proteins for P19735 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P19735
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Spliceosomal protein DIB1
D
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: DIB1 (CDH1, SNU16)
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06819
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 31
F
494Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP31
Find proteins for P49704 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49704
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP3
G
469Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP3 (RNA3)
Find proteins for Q03338 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03338
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing helicase BRR2
B
2163Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BRR2 (RSS1, SNU246)
EC: 3.6.4.13
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32639
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Unknown protein
x
100N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
k, b
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMB1
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
l, h
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD1
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02260
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
m, j
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
n, d
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD3
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43321
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
p, e
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SME1
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
q, f
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX3
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54999
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
r, g
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX2 (SNP2)
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40204
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Snu66
E
328Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU66
Find proteins for Q12420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12420
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
13 kDa ribonucleoprotein-associated protein
K
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU13
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SNU13
Go to UniProtKB:  P39990
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
2
95Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM2 (SMX5, SNP3)
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM2
Go to UniProtKB:  P38203
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3
3
89Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM3 (SMX4, USS2)
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM3
Go to UniProtKB:  P57743
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4
4
187Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM4 (SDB23, USS1)
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM4
Go to UniProtKB:  P40070
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5
5
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM5
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM5
Go to UniProtKB:  P40089
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6
6
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM6
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM6
Go to UniProtKB:  Q06406
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7
7
115Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM7
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM7
Go to UniProtKB:  P53905
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8
8
109Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM8
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM8
Go to UniProtKB:  P47093
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114
C
1008Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU114 (GIN10)
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36048
Entity ID: 1
MoleculeChainsLengthOrganism
U4 snRNAV160Saccharomyces cerevisiae
Entity ID: 2
MoleculeChainsLengthOrganism
U6 snRNAW112Saccharomyces cerevisiae
Entity ID: 19
MoleculeChainsLengthOrganism
U5 snRNAU214Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
E, x
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Advisory, Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2018-03-21
    Type: Other, Structure summary