5GM6

Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 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

Structure of a yeast activated spliceosome at 3.5 angstrom resolution

Yan, C.Wan, R.Bai, R.Huang, G.Shi, Y.

(2016) Science 353: 904-911

  • DOI: 10.1126/science.aag0291

  • PubMed Abstract: 
  • Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome (known as the B(act) complex) from Saccharomyces ce ...

    Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome (known as the B(act) complex) from Saccharomyces cerevisiae, determined by cryo-electron microscopy at an average resolution of 3.52 angstroms. The final refined model contains U2 and U5 small nuclear ribonucleoprotein particles (snRNPs), U6 small nuclear RNA (snRNA), nineteen complex (NTC), NTC-related (NTR) protein, and a 71-nucleotide pre-mRNA molecule, which amount to 13,505 amino acids from 38 proteins and a combined molecular mass of about 1.6 megadaltons. The 5' exon is anchored by loop I of U5 snRNA, whereas the 5' splice site (5'SS) and the branch-point sequence (BPS) of the intron are specifically recognized by U6 and U2 snRNA, respectively. Except for coordination of the catalytic metal ions, the RNA elements at the catalytic cavity of Prp8 are mostly primed for catalysis. The catalytic latency is maintained by the SF3b complex, which encircles the BPS, and the splicing factors Cwc24 and Prp11, which shield the 5' exon-5'SS junction. This structure, together with those determined earlier, outlines a molecular framework for the pre-mRNA splicing reaction.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
2287Saccharomyces 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 helicase BRR2
B
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: 3
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: 6
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RSE1
F
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: 7
MoleculeChainsSequence LengthOrganismDetails
Cold sensitive U2 snRNA suppressor 1
H
436Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CUS1
Find proteins for Q02554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02554
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP11
I
266Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP11 (PRP10, RNA11)
Find proteins for Q07350 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07350
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RDS3
J
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: 10
MoleculeChainsSequence LengthOrganismDetails
RDS3 complex subunit 10
K
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: 14
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP46
O
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: 15
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing protein 45
P
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: 16
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SLT11
Q
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
Pre-mRNA-splicing factor CWC2
R
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: 18
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC15
S
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 BUD31
T
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: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA leakage protein 1
U
207Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PML1
Find proteins for Q07930 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07930
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
U2 snRNP component IST3
V
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: 22
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC26
W
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: 23
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
Y
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: 24
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC22
Z
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: 25
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC24
a
259Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CWC24
Find proteins for P53769 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53769
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl isomerase CWC27
b
301Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CWC27 (CYP7)
EC: 5.2.1.8
Find proteins for Q02770 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q02770
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CEF1
c
587Saccharomyces 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: 28
MoleculeChainsSequence LengthOrganismDetails
U2 snRNP component HSH155
G
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: 29
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CLF1
d
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: 30
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC21
X
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: 31
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1
v
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: 32
MoleculeChainsSequence LengthOrganismDetails
Protein HSH49
e
213Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: HSH49
Find proteins for Q99181 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q99181
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF2
f
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SYF2 (NTC31)
Find proteins for P53277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SYF2
Go to UniProtKB:  P53277
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
o, p, q, r
503Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP19 (PSO4)
EC: 2.3.2.27
Find proteins for P32523 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32523
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNT309
t
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SNT309 (NTC25)
Find proteins for Q06091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06091
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
n
455Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CDC40 (PRP17, SLU4, XRS2)
Find proteins for P40968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CDC40
Go to UniProtKB:  P40968
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein 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: 38
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
i
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: 39
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
h
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: 40
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
j
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: 41
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
l
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: 42
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
m
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: 43
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
g
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217
Entity ID: 4
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae strain CDRDR_sf_H chromosome VII sequenceD214Saccharomyces cerevisiae
Entity ID: 5
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae strain T.52_2H chromosome XII sequenceE112Saccharomyces cerevisiae
Entity ID: 11
MoleculeChainsLengthOrganism
U2 snRNAL1175Saccharomyces cerevisiae S288C
Entity ID: 12
MoleculeChainsLengthOrganism
Pre-mRNAN25Saccharomyces cerevisiae S288C
Entity ID: 13
MoleculeChainsLengthOrganism
Pre-mRNAM61Saccharomyces cerevisiae S288C
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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a, I, J, Q, R, T
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

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Y
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
GTP
Query on GTP

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

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E, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
c, d, v
L-PEPTIDE LINKINGC4 H9 N O2

--

N
Query on N
M
RNA LINKINGC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Other