5NRL

Structure of a pre-catalytic spliceosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.5 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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7
7
115Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53905

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8
8
109Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
2413Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114
C
1008Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 31
F
494Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49704 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP3
G
469Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q03338 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03338

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
13 kDa ribonucleoprotein-associated protein
K
126Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
23 kDa U4/U6.U5 small nuclear ribonucleoprotein component
L
194Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 38
M
242Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q00723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RSE1
P
1361Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q04693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Cold sensitive U2 snRNA suppressor 1
Q
435Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Protein HSH49
R
213Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q99181 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RDS3
S
107Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06835 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP9
T
530Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P19736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP11
U
266Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q07350 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP21
V
280Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P32524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
W
238Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Unknown
X
111Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
b, k, s
196Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
d, n, v
101Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e, p, w
94Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f, q, x
86Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g, r, y
77Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
h, l, t
146Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6
z
86Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for A6ZYX7 (Saccharomyces cerevisiae (strain YJM789))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Spliceosomal protein DIB1
D
143Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
E
587Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP4
H
465Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 6
J
899Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P19735 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3
3
89Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SPP381
N
291Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38282 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
U2 snRNP component HSH155
O
971Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
Y
111Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RDS3 complex subunit 10
Z
85Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C074 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
a
95Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
i, m, u
110Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4
j
187Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40070

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5
o
93Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40089

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing helicase BRR2
B
2163Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32639

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Entity ID: 1
MoleculeChainsLengthOrganism
U2 snRNA21175Saccharomyces cerevisiae

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Entity ID: 3
MoleculeChainsLengthOrganism
U4 snRNA4160Saccharomyces cerevisiae

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Entity ID: 4
MoleculeChainsLengthOrganism
U5 snRNA5214Saccharomyces cerevisiae

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Entity ID: 16
MoleculeChainsLengthOrganism
Yeast UBC4 gene for ubiquitin-conjugating enzymeI95Saccharomyces cerevisiae

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Entity ID: 5
MoleculeChainsLengthOrganism
U6 snRNA6112Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

Download CCD File 
L, S, T, U
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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
    Changes: Database references, Derived calculations
  • Version 1.2: 2017-07-19
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2018-03-21
    Changes: Advisory, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.5: 2018-11-28
    Changes: Advisory, Data collection, Database references, Derived calculations