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 spp42A2363Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: spp42cwf6SPAC4F8.12c
UniProt
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
UniProt
Find proteins for O94316 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3D, JA [auth Z]97Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smd3SPBC19C2.14
UniProt
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, KA [auth b]147Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smb1SPAC26A3.08
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1F, LA [auth f]117Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smd1SPAC27D7.07c
UniProt
Find proteins for O42661 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2G, MA [auth l]115Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smd2cwf9SPAC2C4.03c
UniProt
Find proteins for O14036 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EH, NA [auth m]84Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: sme1SPBC11G11.06c
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FI, OA [auth n]78Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smf1SPBC3E7.14SPBC4F6.01
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GJ, PA [auth o]77Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smg1SPBC4B4.05
UniProt
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
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf17L340Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf17SPBC1289.11
UniProt
Find proteins for O94620 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45M557Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp45cwf13snw1SPCC188.11SPCC584.08
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19R [auth S], S [auth T], T [auth U], U [auth V]488Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp19cwf8SPAC29A4.08c
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cdc5V [auth W]757Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cdc5SPAC644.12
UniProt
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Entity ID: 20
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Pre-mRNA-splicing factor cwf2W [auth Y]388Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf2prp3SPAC3A12.11c
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf5X [auth a]354Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf5ecm2SPCC550.02c
UniProt
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf19Y [auth c]639Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf19SPAC30D11.09
UniProt
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase ppi1Z [auth d]155Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ppi1cyp2SPAC57A10.03
EC: 5.2.1.8
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf14AA [auth e]146Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf14SPBC24C6.11
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17BA [auth g]558Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp17SPBC6B1.10
UniProt
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Entity ID: 26
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Pre-mRNA-splicing factor cwf15CA [auth h]265Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf15SPBC337.06c
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf7DA [auth i]187Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf7spf27SPBC28F2.04c
UniProt
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf4EA [auth R]674Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf4syf3SPBC31F10.11c
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf3FA [auth r]790Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf3syf1SPBC211.02c
UniProt
Find proteins for Q9P7R9 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf11GA [auth X]1284Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cwf11SPBC646.02
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'HA [auth j]239Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lea1SPBC1861.08c
UniProt
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Probable U2 small nuclear ribonucleoprotein B''IA [auth k]111Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: msl1pi056SPBC8D2.09c
UniProt
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
unknown chainQA [auth x]412Schizosaccharomyces 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')P [auth Q]13Schizosaccharomyces pombe
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      Entity ID: 17
      MoleculeChainsLengthOrganismImage
      U2 snRNAQ [auth P]186Schizosaccharomyces pombe
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      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      GDP
      Query on GDP

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

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

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      AB [auth e], BB [auth e], CB [auth e], WA [auth Y], XA [auth a], YA [auth a], ZA [auth c]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

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      SA [auth N], TA [auth N], UA [auth N], VA [auth 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  (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