5LQW

yeast activated spliceosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular architecture of the Saccharomyces cerevisiae activated spliceosome

Rauhut, R.Fabrizio, P.Dybkov, O.Hartmuth, K.Pena, V.Chari, A.Kumar, V.Lee, C.T.Urlaub, H.Kastner, B.Stark, H.Luehrmann, R.

(2016) Science 6306: 1399-1405

  • DOI: 10.1126/science.aag1906
  • Primary Citation of Related Structures:  
    5LQW

  • PubMed Abstract: 
  • The activated spliceosome (B act ) is in a catalytically inactive state and is remodeled into a catalytically active machine by the RNA helicase Prp2, but the mechanism is unclear. Here, we describe a 3D electron cryomicroscopy structure of the Saccharomyces cerevisiae B act complex at 5 ...

    The activated spliceosome (B act ) is in a catalytically inactive state and is remodeled into a catalytically active machine by the RNA helicase Prp2, but the mechanism is unclear. Here, we describe a 3D electron cryomicroscopy structure of the Saccharomyces cerevisiae B act complex at 5.8-angstrom resolution. Our model reveals that in B act , the catalytic U2/U6 RNA-Prp8 ribonucleoprotein core is already established, and the 5' splice site (ss) is oriented for step 1 catalysis but occluded by protein. The first-step nucleophile-the branchsite adenosine-is sequestered within the Hsh155 HEAT domain and is held 50 angstroms away from the 5'ss. Our structure suggests that Prp2 adenosine triphosphatase-mediated remodeling leads to conformational changes in Hsh155's HEAT domain that liberate the first-step reactants for catalysis.


    Organizational Affiliation

    Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. b.kastner@mpi-bpc.mpg.de hstark1@gwdg.de reinhard.luehrmann@mpi-bpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8A2,413Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
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Pre-mRNA-splicing factor SNU114B1,008Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing helicase BRR2C2,163Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13
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Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11D364Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31E157Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2F339Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
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Pre-mRNA-splicing factor CWC22G [auth H]577Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U2 snRNP component IST3H [auth J]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46I [auth K]451Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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Pre-mRNA-splicing factor CWC26J [auth L]266Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45K [auth M]379Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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Pre-mRNA leakage protein 1L [auth N]204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2M [auth O]876Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRP2RNA2YNR011CN2048
EC: 3.6.4.13
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Entity ID: 14
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Pre-mRNA-splicing factor SYF1N [auth P]859Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
U2 snRNP component HSH155O [auth Q]971Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
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Pre-mRNA-splicing factor CLF1P [auth R]687Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
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Pre-mRNA-splicing factor CEF1Q [auth W]590Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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Pre-mRNA-splicing factor RSE1R [auth X]1,361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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Pre-mRNA-splicing factor RDS3S [auth Y]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
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RDS3 complex subunit 10T [auth Z]85Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P0C074 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
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Small nuclear ribonucleoprotein-associated protein BU [auth b]196Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3V [auth d]101Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EW [auth e]94Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FX [auth f]86Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GY [auth g]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1Z [auth h]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
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Small nuclear ribonucleoprotein Sm D2AA [auth j]110Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsLengthOrganismImage
U2 snRNABA [auth 2]1,175Saccharomyces cerevisiae
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Entity ID: 29
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U5 snRNACA [auth 5]179Saccharomyces cerevisiae
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Entity ID: 30
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U6 snRNADA [auth 6]112Saccharomyces cerevisiae
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Entity ID: 31
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actin pre-mRNAEA [auth 9]572Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 860

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations