3JCM | pdb_00003jcm

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

Validation slider image for 3JCM

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 1,373.83 kDa 
  • Atom Count: 58,253 
  • Modeled Residue Count: 8,679 
  • Deposited Residue Count: 11,080 
  • Unique protein chains: 23
  • Unique nucleic acid chains: 4

Macromolecules


Find similar proteins by:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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:|  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
Entity ID: 24
MoleculeChains LengthOrganismImage
pre-mRNAEA [auth C]20synthetic construct
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
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) 
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) 
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
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Other