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 8 A2413Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114 B1008Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
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Pre-mRNA-splicing helicase BRR2 C2163Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11 D364Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31 E157Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P25337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2 F339Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 H577Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U2 snRNP component IST3 J148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46 K451Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC26 L266Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P46947 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45 M379Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA leakage protein 1 N204Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q07930 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
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Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 O876Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRP2, RNA2, YNR011C, N2048
EC: 3.6.4.13
Find proteins for P20095 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1 P859Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
U2 snRNP component HSH155 Q971Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1 R687Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1 W590Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RSE1 X1361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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Pre-mRNA-splicing factor RDS3 Y107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
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RDS3 complex subunit 10 Z85Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein B b196Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 d101Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
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Small nuclear ribonucleoprotein E e94Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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Small nuclear ribonucleoprotein F f86Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
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Small nuclear ribonucleoprotein G g77Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
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Small nuclear ribonucleoprotein Sm D1 h146Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
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Small nuclear ribonucleoprotein Sm D2 j110Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsLengthOrganismImage
U2 snRNA21175Saccharomyces cerevisiae
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Entity ID: 29
MoleculeChainsLengthOrganismImage
U5 snRNA5179Saccharomyces cerevisiae
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Entity ID: 30
MoleculeChainsLengthOrganismImage
U6 snRNA6112Saccharomyces cerevisiae
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Entity ID: 31
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actin pre-mRNA9572Saccharomyces cerevisiae
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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View more in-depth experimental data

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