5LJ3

Structure of the core of the yeast spliceosome immediately after branching


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structure of the spliceosome immediately after branching.

Galej, W.P.Wilkinson, M.E.Fica, S.M.Oubridge, C.Newman, A.J.Nagai, K.

(2016) Nature 537: 197-201

  • DOI: 10.1038/nature19316
  • Primary Citation of Related Structures:  
  • Also Cited By: 5MQ0, 5MPS

  • PubMed Abstract: 
  • Precursor mRNA (pre-mRNA) splicing proceeds by two consecutive transesterification reactions via a lariat-intron intermediate. Here we present the 3.8 Å cryo-electron microscopy structure of the spliceosome immediately after lariat formation. The 5'- ...

    Precursor mRNA (pre-mRNA) splicing proceeds by two consecutive transesterification reactions via a lariat-intron intermediate. Here we present the 3.8 Å cryo-electron microscopy structure of the spliceosome immediately after lariat formation. The 5'-splice site is cleaved but remains close to the catalytic Mg2+ site in the U2/U6 small nuclear RNA (snRNA) triplex, and the 5'-phosphate of the intron nucleotide G(+1) is linked to the branch adenosine 2'OH. The 5'-exon is held between the Prp8 amino-terminal and linker domains, and base-pairs with U5 snRNA loop 1. Non-Watson-Crick interactions between the branch helix and 5'-splice site dock the branch adenosine into the active site, while intron nucleotides +3 to +6 base-pair with the U6 snRNA ACAGAGA sequence. Isy1 and the step-one factors Yju2 and Cwc25 stabilize docking of the branch helix. The intron downstream of the branch site emerges between the Prp8 reverse transcriptase and linker domains and extends towards the Prp16 helicase, suggesting a plausible mechanism of remodelling before exon ligation.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 6
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: 7
MoleculeChainsSequence LengthOrganismDetails
Protein CWC16
D
278Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: YJU2 (CWC16)
Find proteins for P28320 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P28320
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC25
F
179Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CWC25
Find proteins for P53854 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CWC25
Go to UniProtKB:  P53854
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114
C
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: 10
MoleculeChainsSequence LengthOrganismDetails
ISY1
G
235Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ISY1 (NTC30, UTR3)
Find proteins for P21374 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ISY1
Go to UniProtKB:  P21374
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
CWC22
H
591N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PRP46
J
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: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing protein 45
K
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: 14
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor BUD31
L
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: 15
MoleculeChainsSequence LengthOrganismDetails
CWC2
M
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: 16
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SLT11
N
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: 17
MoleculeChainsSequence LengthOrganismDetails
CEF1
O
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
CWC15
P
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CWC15
Find proteins for Q03772 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CWC15
Go to UniProtKB:  Q03772
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC21
R
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CWC21
Find proteins for Q03375 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03375
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
CLF1
S
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: 21
MoleculeChainsSequence LengthOrganismDetails
SYF1
T
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: 22
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
b, k
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: 23
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
d, n
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: 24
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e, p
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: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f, q
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: 26
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g, r
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: 27
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
h, l
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: 28
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
j, m
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: 29
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
W
238Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LEA1
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08963
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
Y
111Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: MSL1
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MSL1
Go to UniProtKB:  P40567
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
unknown
x
132N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
U5 snRNA (small nuclear RNA)U179Saccharomyces cerevisiae
Entity ID: 2
MoleculeChainsLengthOrganism
Exon 1 (5' exon) of UBC4 pre-mRNAE16Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
Intron of UBC4 pre-mRNAI76Saccharomyces cerevisiae
Entity ID: 4
MoleculeChainsLengthOrganism
U2 snRNA (small nuclear RNA)Z1175Saccharomyces cerevisiae
Entity ID: 5
MoleculeChainsLengthOrganism
U6 snRNA (small nuclear RNA)V112Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, L, M, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
E, V
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
x
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-09-21
    Type: Database references
  • Version 1.2: 2017-08-30
    Type: Data collection, Derived calculations