3JB9

Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.0 of the entry. See complete history


Literature

Structure of a yeast spliceosome at 3.6-angstrom resolution

Yan, C.Hang, J.Wan, R.Huang, M.Wong, C.Shi, Y.

(2015) Science 349: 1182-1191

  • DOI: 10.1126/science.aac7629
  • Primary Citation of Related Structures:  
    3JB9

  • PubMed Abstract: 
  • Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors ...

    Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors. Here, we report the three-dimensional structure of a Schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. This spliceosome contains U2 and U5 snRNPs, NTC, NTR, U6 small nuclear RNA, and an RNA intron lariat. The atomic model includes 10,574 amino acids from 37 proteins and four RNA molecules, with a combined molecular mass of approximately 1.3 megadaltons. Spp42 (Prp8 in Saccharomyces cerevisiae), the key protein component of the U5 snRNP, forms a central scaffold and anchors the catalytic center. Both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mRNA splicing. Our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of pre-mRNA splicing.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, 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 spp42 A2363Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: spp42cwf6SPAC4F8.12c
Find proteins for O14187 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf10 B984Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf10snu114spef2SPBC215.12
Find proteins for O94316 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 DZ97Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smd3SPBC19C2.14
Find proteins for Q9UUC6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein B Eb147Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smb1SPAC26A3.08
Find proteins for Q10163 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1 Ff117Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smd1SPAC27D7.07c
Find proteins for O42661 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2 Gl115Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smd2cwf9SPAC2C4.03c
Find proteins for O14036 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E Hm84Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: sme1SPBC11G11.06c
Find proteins for Q9USZ3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F In78Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smf1SPBC3E7.14SPBC4F6.01
Find proteins for O59734 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein G Jo77Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smg1SPBC4B4.05
Find proteins for O74966 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor prp5 K473Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp5cwf1pi024SPBP22H7.07
Find proteins for O13615 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf17 L340Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf17SPBC1289.11
Find proteins for O94620 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45 M557Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp45cwf13snw1SPCC188.11SPCC584.08
Find proteins for Q09882 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19 STUV488Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp19cwf8SPAC29A4.08c
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for O14011 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cdc5 W757Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cdc5SPAC644.12
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf2 Y388Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf2prp3SPAC3A12.11c
Find proteins for P87126 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 21
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Pre-mRNA-splicing factor cwf5 a354Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf5ecm2SPCC550.02c
Find proteins for O59800 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf19 c639Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf19SPAC30D11.09
Find proteins for Q09909 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase ppi1 d155Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ppi1cyp2SPAC57A10.03
EC: 5.2.1.8
Find proteins for P87051 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf14 e146Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf14SPBC24C6.11
Find proteins for O74772 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17 g558Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp17SPBC6B1.10
Find proteins for O43071 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf15 h265Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf15SPBC337.06c
Find proteins for P78794 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 27
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Pre-mRNA-splicing factor cwf7 i187Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf7spf27SPBC28F2.04c
Find proteins for Q9USV3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf4 R674Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf4syf3SPBC31F10.11c
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Entity ID: 29
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Pre-mRNA-splicing factor cwf3 r790Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf3syf1SPBC211.02c
Find proteins for Q9P7R9 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 30
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Pre-mRNA-splicing factor cwf11 X1284Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf11SPBC646.02
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A' j239Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lea1SPBC1861.08c
Find proteins for Q9USX8 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Probable U2 small nuclear ribonucleoprotein B'' k111Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: msl1pi056SPBC8D2.09c
Find proteins for Q7LL14 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
unknown chain x412Schizosaccharomyces pombe 972h-Mutation(s): 0 
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Entity ID: 3
MoleculeChainsLengthOrganismImage
U5 snRNAC120Schizosaccharomyces pombe
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Entity ID: 14
MoleculeChainsLengthOrganismImage
U6 snRNAN99Schizosaccharomyces pombe
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  • Entity ID: 15
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*GP*UP*AP*UP*GP*UP*AP*U)-3')O8Schizosaccharomyces pombe
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    • Entity ID: 16
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(P*UP*UP*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*C)-3')Q13Schizosaccharomyces pombe
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      Entity ID: 17
      MoleculeChainsLengthOrganismImage
      U2 snRNAP186Schizosaccharomyces pombe
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 3.60 Å
      • Aggregation State: PARTICLE 
      • Reconstruction Method: SINGLE PARTICLE 

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2015-09-23
        Type: Initial release
      • Version 1.1: 2019-10-16
        Changes: Data collection, Database references, Derived calculations, Other
      • Version 2.0: 2019-12-11
        Changes: Advisory, Atomic model, Data collection, Derived calculations, Other