3JCM

Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

The 3.8 angstrom structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis

Wan, R.Yan, C.Bai, R.Wang, L.Huang, M.Wong, C.C.Shi, Y.

(2016) Science 351: 466-475

  • DOI: https://doi.org/10.1126/science.aad6466
  • Primary Citation of Related Structures:  
    3JCM

  • PubMed Abstract: 

    Splicing of precursor messenger RNA is accomplished by a dynamic megacomplex known as the spliceosome. Assembly of a functional spliceosome requires a preassembled U4/U6.U5 tri-snRNP complex, which comprises the U5 small nuclear ribonucleoprotein (snRNP), the U4 and U6 small nuclear RNA (snRNA) duplex, and a number of protein factors. Here we report the three-dimensional structure of a Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at an overall resolution of 3.8 angstroms by single-particle electron cryomicroscopy. The local resolution for the core regions of the tri-snRNP reaches 3.0 to 3.5 angstroms, allowing construction of a refined atomic model. Our structure contains U5 snRNA, the extensively base-paired U4/U6 snRNA, and 30 proteins including Prp8 and Snu114, which amount to 8495 amino acids and 263 nucleotides with a combined molecular mass of ~1 megadalton. The catalytic nucleotide U80 from U6 snRNA exists in an inactive conformation, stabilized by its base-pairing interactions with U4 snRNA and protected by Prp3. Pre-messenger RNA is bound in the tri-snRNP through base-pairing interactions with U6 snRNA and loop I of U5 snRNA. This structure, together with that of the spliceosome, reveals the molecular choreography of the snRNAs in the activation process of the spliceosomal ribozyme.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 82,413Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33334 
Go to UniProtKB:  P33334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33334
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP4465Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P20053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20053 
Go to UniProtKB:  P20053
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20053
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 31C [auth I]494Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P49704 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49704 
Go to UniProtKB:  P49704
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49704
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 6D [auth G]899Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P19735 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P19735 
Go to UniProtKB:  P19735
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19735
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP3E [auth K]469Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q03338 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03338 
Go to UniProtKB:  Q03338
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03338
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosomal protein DIB1F [auth L]143Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06819 
Go to UniProtKB:  Q06819
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06819
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinG [auth M]126Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39990 
Go to UniProtKB:  P39990
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39990
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU1141,008Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36048 
Go to UniProtKB:  P36048
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36048
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing helicase BRR2I [auth N]2,163Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32639 
Go to UniProtKB:  P32639
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32639
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3J [auth R],
Q [auth J]
101Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43321 
Go to UniProtKB:  P43321
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43321
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BK [auth S],
R [auth O]
196Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40018 
Go to UniProtKB:  P40018
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40018
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1L [auth T],
S [auth P]
146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02260 
Go to UniProtKB:  Q02260
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02260
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2M [auth U],
T [auth Q]
110Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06217 
Go to UniProtKB:  Q06217
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06217
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EN [auth V],
U [auth Y]
94Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12330 
Go to UniProtKB:  Q12330
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12330
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FO [auth W],
V [auth Z]
86Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54999 
Go to UniProtKB:  P54999
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54999
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GP [auth X],
W [auth a]
77Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40204 
Go to UniProtKB:  P40204
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40204
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8X [auth b]109Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47093 
Go to UniProtKB:  P47093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47093
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2Y [auth c]95Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38203 
Go to UniProtKB:  P38203
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38203
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3Z [auth d]89Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P57743 
Go to UniProtKB:  P57743
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP57743
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6AA [auth e]86Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06406 
Go to UniProtKB:  Q06406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06406
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5BA [auth f]93Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40089 
Go to UniProtKB:  P40089
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40089
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7CA [auth g]115Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53905 
Go to UniProtKB:  P53905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53905
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4DA [auth h]187Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40070 
Go to UniProtKB:  P40070
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40070
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 24
MoleculeChains LengthOrganismImage
pre-mRNAEA [auth C]20synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains LengthOrganismImage
SNR6 snRNAFA [auth D]112Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains LengthOrganismImage
SNR14 snRNAGA [auth E]160Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains LengthOrganismImage
SNR7-L snRNAHA [auth F]214Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
IA [auth H]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
M7M
Query on M7M

Download Ideal Coordinates CCD File 
JA [auth E]N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)
C13 H23 N5 O11 P2
DHQQIEJARUGVNZ-WOUKDFQISA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references, Derived calculations, Other