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


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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: 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 (sn ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8A2413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP4B465Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP4RNA4YPR178WP9705.6
Find proteins for P20053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 31I494Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP31YGR091W
Find proteins for P49704 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 6G899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP6RNA6YBR055CYBR0508
Find proteins for P19735 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP3K469Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP3RNA3YDR473CD8035.16
Find proteins for Q03338 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosomal protein DIB1L143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIB1CDH1SNU16YPR082CP9513.12
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinM126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114H1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing helicase BRR2N2163Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRR2RSS1SNU246YER172CSYGP-ORF66
EC: 3.6.4.13
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3JR101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BOS196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1PT146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2QU110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EVY94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FWZ86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GXa77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8b109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM8YJR022WJ1464YJR83.16
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2c95Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM2SMX5SNP3YBL026WYBL0425
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3d89Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM3SMX4USS2YLR438C-A
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6e86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM6YDR378CD9481.18
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5f93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM5YER146W
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7g115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM7YNL147WN1202N1780
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4h187Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM4SDB23USS1YER112W
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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  • Entity ID: 24
    MoleculeChainsLengthOrganismImage
    pre-mRNAC20synthetic construct
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    Entity ID: 25
    MoleculeChainsLengthOrganismImage
    SNR6 snRNAD112Saccharomyces cerevisiae S288C
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    Entity ID: 26
    MoleculeChainsLengthOrganismImage
    SNR14 snRNAE160Saccharomyces cerevisiae S288C
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    Entity ID: 27
    MoleculeChainsLengthOrganismImage
    SNR7-L snRNAF214Saccharomyces cerevisiae S288C
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GTP
    Query on GTP

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    H
    GUANOSINE-5'-TRIPHOSPHATE
    C10 H16 N5 O14 P3
    XKMLYUALXHKNFT-UUOKFMHZSA-N
     Ligand Interaction
    M7M
    Query on M7M

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    E
    N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)
    C13 H23 N5 O11 P2
    DHQQIEJARUGVNZ-WOUKDFQISA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

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

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

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