5NRL

Structure of a pre-catalytic spliceosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of a pre-catalytic spliceosome.

Plaschka, C.Lin, P.C.Nagai, K.

(2017) Nature 546: 617-621

  • DOI: 10.1038/nature22799

  • PubMed Abstract: 
  • Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae pre-cat ...

    Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae pre-catalytic B complex spliceosome at near-atomic resolution. The mobile U2 small nuclear ribonucleoprotein particle (snRNP) associates with U4/U6.U5 tri-snRNP through the U2/U6 helix II and an interface between U4/U6 di-snRNP and the U2 snRNP SF3b-containing domain, which also transiently contacts the helicase Brr2. The 3' region of the U2 snRNP is flexibly attached to the SF3b-containing domain and protrudes over the concave surface of tri-snRNP, where the U1 snRNP may reside before its release from the pre-mRNA 5' splice site. The U6 ACAGAGA sequence forms a hairpin that weakly tethers the 5' splice site. The B complex proteins Prp38, Snu23 and Spp381 bind the Prp8 N-terminal domain and stabilize U6 ACAGAGA stem-pre-mRNA and Brr2-U4 small nuclear RNA interactions. These results provide important insights into the events leading to active site formation.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3
3
89Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM3 (SMX4, USS2)
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM3
Go to UniProtKB:  P57743
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7
7
115Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM7
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM7
Go to UniProtKB:  P53905
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8
8
109Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM8
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM8
Go to UniProtKB:  P47093
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
2413Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP8 (DBF3, DNA39, RNA8, SLT21, USA2)
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33334
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing helicase BRR2
B
2163Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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: 10
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114
C
1008Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU114 (GIN10)
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36048
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Spliceosomal protein DIB1
D
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: DIB1 (CDH1, SNU16)
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06819
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
E
587Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU66
Find proteins for Q12420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12420
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 31
F
494Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP31
Find proteins for P49704 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49704
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP3
G
469Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP3 (RNA3)
Find proteins for Q03338 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03338
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP4
H
465Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP4 (RNA4)
Find proteins for P20053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20053
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 6
J
899Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP6 (RNA6)
Find proteins for P19735 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P19735
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
13 kDa ribonucleoprotein-associated protein
K
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU13
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SNU13
Go to UniProtKB:  P39990
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
23 kDa U4/U6.U5 small nuclear ribonucleoprotein component
L
194Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU23
Find proteins for Q12368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12368
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 38
M
242Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP38
Find proteins for Q00723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q00723
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SPP381
N
291Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPP381
Find proteins for P38282 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38282
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
U2 snRNP component HSH155
O
971Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HSH155
Find proteins for P49955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49955
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RSE1
P
1361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RSE1 (SAP130)
Find proteins for Q04693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04693
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Cold sensitive U2 snRNA suppressor 1
Q
435Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CUS1
Find proteins for Q02554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02554
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Protein HSH49
R
213Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HSH49
Find proteins for Q99181 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q99181
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RDS3
S
107Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RDS3
Find proteins for Q06835 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06835
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP9
T
530Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP9
Find proteins for P19736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P19736
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP11
U
266Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP11 (PRP10, RNA11)
Find proteins for Q07350 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07350
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP21
V
280Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP21 (SPP91)
Find proteins for P32524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32524
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
W
238Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LEA1
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08963
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Unknown
X
111N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
Y
111Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MSL1
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MSL1
Go to UniProtKB:  P40567
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RDS3 complex subunit 10
Z
85Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: YSF3 (RCP10)
Find proteins for P0C074 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C074
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
a
95Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM2 (SMX5, SNP3)
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM2
Go to UniProtKB:  P38203
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
b, k, s
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMB1
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
d, n, v
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD3
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43321
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e, p, w
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SME1
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f, q, x
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX3
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54999
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g, r, y
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX2 (SNP2)
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40204
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
h, l, t
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD1
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02260
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
i, m, u
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4
j
187Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM4 (SDB23, USS1)
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM4
Go to UniProtKB:  P40070
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5
o
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM5
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM5
Go to UniProtKB:  P40089
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6
z
86Saccharomyces cerevisiae (strain YJM789)Mutation(s): 0 
Gene Names: LSM6
Find proteins for A6ZYX7 (Saccharomyces cerevisiae (strain YJM789))
Go to Gene View: LSM6
Go to UniProtKB:  A6ZYX7
Entity ID: 1
MoleculeChainsLengthOrganism
U2 snRNA21175Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
U4 snRNA4160Saccharomyces cerevisiae
Entity ID: 4
MoleculeChainsLengthOrganism
U5 snRNA5214Saccharomyces cerevisiae
Entity ID: 5
MoleculeChainsLengthOrganism
U6 snRNA6112Saccharomyces cerevisiae
Entity ID: 16
MoleculeChainsLengthOrganism
Yeast UBC4 gene for ubiquitin-conjugating enzymeI95Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
L, S, T, U
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
2
RNA LINKINGC9 H13 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184330
European Research CouncilUnited Kingdom693087 - SPLICE3D

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references, Derived calculations
  • Version 1.2: 2017-07-19
    Type: Database references
  • Version 1.3: 2017-08-30
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2018-03-21
    Type: Advisory, Derived calculations, Source and taxonomy, Structure summary