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 

wwPDB Validation 3D Report Full Report



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 cofac ...

    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 spp42A2363Schizosaccharomyces 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 cwf10B984Schizosaccharomyces 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 D3D, Z97Schizosaccharomyces 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 BE, b147Schizosaccharomyces 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: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2G, l115Schizosaccharomyces 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 EH, m84Schizosaccharomyces 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 FI, n78Schizosaccharomyces 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 GJ, o77Schizosaccharomyces 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 prp5K473Schizosaccharomyces 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 cwf17L340Schizosaccharomyces 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: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19S, T, U, V488Schizosaccharomyces 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 cdc5W757Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cdc5SPAC644.12
Find proteins for P39964 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf2Y388Schizosaccharomyces 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
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf5a354Schizosaccharomyces 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 cwf19c639Schizosaccharomyces 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 ppi1d155Schizosaccharomyces 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 cwf14e146Schizosaccharomyces 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 17g558Schizosaccharomyces 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 cwf15h265Schizosaccharomyces 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
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf7i187Schizosaccharomyces 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 cwf4R674Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf4syf3SPBC31F10.11c
Find proteins for P87312 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf3r790Schizosaccharomyces 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
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf11X1284Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf11SPBC646.02
Find proteins for O94508 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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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 chainx412Schizosaccharomyces pombe 972h-Mutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45M557Schizosaccharomyces 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: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1F, f117Schizosaccharomyces 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: 15
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*GP*UP*AP*UP*GP*UP*AP*U)-3')O8Schizosaccharomyces pombe
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    Entity ID: 17
    MoleculeChainsLengthOrganismImage
    U2 snRNAP186Schizosaccharomyces pombe
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    Entity ID: 14
    MoleculeChainsLengthOrganismImage
    U6 snRNAN99Schizosaccharomyces 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: 3
      MoleculeChainsLengthOrganismImage
      U5 snRNAC120Schizosaccharomyces pombe
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      GDP
      Query on GDP

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      B
      GUANOSINE-5'-DIPHOSPHATE
      C10 H15 N5 O11 P2
      QGWNDRXFNXRZMB-UUOKFMHZSA-N
       Ligand Interaction
      ADP
      Query on ADP

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      X
      ADENOSINE-5'-DIPHOSPHATE
      C10 H15 N5 O10 P2
      XTWYTFMLZFPYCI-KQYNXXCUSA-N
       Ligand Interaction
      ZN
      Query on ZN

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      Y, a, c, e
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

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      N
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      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 

      • 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