5LQW

yeast activated spliceosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • PubMed Abstract: 
  • The activated spliceosome (Bact) 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 Sacchar ...

    The activated spliceosome (Bact) 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 Bact complex at 5.8-angstrom resolution. Our model reveals that in Bact, 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
2413Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP8 (DBF3, DNA39, RNA8, SLT21, USA2)
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33334
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114
B
1008Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SNU114 (GIN10)
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36048
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing helicase BRR2
C
2163Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: BRR2 (RSS1, SNU246)
EC: 3.6.4.13
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32639
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SLT11
D
364Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ECM2 (SLT11)
Find proteins for P38241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ECM2
Go to UniProtKB:  P38241
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor BUD31
E
157Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: BUD31 (CWC14)
Find proteins for P25337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: BUD31
Go to UniProtKB:  P25337
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC2
F
339Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CWC2 (NTC40, SLC3)
Find proteins for Q12046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12046
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC22
H
577Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CWC22
Find proteins for P53333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CWC22
Go to UniProtKB:  P53333
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
U2 snRNP component IST3
J
148Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: IST3 (SNU17)
Find proteins for P40565 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40565
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP46
K
451Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP46 (CWC1, NTC50)
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12417
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC26
L
266Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: BUD13 (CWC26, SLC7)
Find proteins for P46947 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: BUD13
Go to UniProtKB:  P46947
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing protein 45
M
379Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP45 (FUN20)
Find proteins for P28004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P28004
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA leakage protein 1
N
204Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PML1
Find proteins for Q07930 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07930
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
O
876Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP2 (RNA2)
EC: 3.6.4.13
Find proteins for P20095 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20095
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1
P
859Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SYF1 (NTC90)
Find proteins for Q04048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04048
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
U2 snRNP component HSH155
Q
971Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: HSH155
Find proteins for P49955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49955
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CLF1
R
687Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CLF1 (NTC77, SYF3)
Find proteins for Q12309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12309
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CEF1
W
590Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CEF1 (NTC85)
Find proteins for Q03654 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03654
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RSE1
X
1361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RSE1 (SAP130)
Find proteins for Q04693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04693
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RDS3
Y
107Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RDS3
Find proteins for Q06835 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06835
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RDS3 complex subunit 10
Z
85Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: YSF3 (RCP10)
Find proteins for P0C074 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C074
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
b
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMB1
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
d
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMD3
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43321
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SME1
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMX3
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54999
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMX2 (SNP2)
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40204
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
h
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMD1
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02260
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
j
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217
Entity ID: 28
MoleculeChainsLengthOrganism
U2 snRNA21175Saccharomyces cerevisiae
Entity ID: 29
MoleculeChainsLengthOrganism
U5 snRNA5179Saccharomyces cerevisiae
Entity ID: 30
MoleculeChainsLengthOrganism
U6 snRNA6112Saccharomyces cerevisiae
Entity ID: 31
MoleculeChainsLengthOrganism
actin pre-mRNA9572Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
German Research FoundationGermanySFB 860

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence, Data collection, Derived calculations