7DCO | pdb_00007dco

Cryo-EM structure of the activated spliceosome (Bact complex) at an atomic resolution of 2.5 angstrom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2.

Bai, R.Wan, R.Yan, C.Jia, Q.Lei, J.Shi, Y.

(2021) Science 371

  • DOI: https://doi.org/10.1126/science.abe8863
  • Primary Citation Related Structures: 
    7DCO, 7DCP, 7DCQ, 7DCR, 7DD3

  • PubMed Abstract: 

    Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the function of the ATPase/helicases remains poorly understood. Here, we report atomic structures of Prp2 in isolation, Prp2 complexed with its coactivator Spp2, and Prp2-loaded activated spliceosome and the results of structure-guided biochemical analysis. Prp2 weakly associates with the spliceosome and cannot function without Spp2, which stably associates with Prp2 and anchors on the spliceosome, thus tethering Prp2 to the activated spliceosome and allowing Prp2 to function. Pre-mRNA is loaded into a featured channel between the N and C halves of Prp2, where Leu 536 from the N half and Arg 844 from the C half prevent backward sliding of pre-mRNA toward its 5'-end. Adenosine 5'-triphosphate binding and hydrolysis trigger interdomain movement in Prp2, which drives unidirectional stepwise translocation of pre-mRNA toward its 3'-end. These conserved mechanisms explain the coupling of spliceosome remodeling to pre-mRNA splicing.


  • Organizational Affiliation
    • Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China.

Macromolecule Content 

  • Total Structure Weight: 2,914.32 kDa 
  • Atom Count: 129,875 
  • Modeled Residue Count: 15,850 
  • Deposited Residue Count: 22,483 
  • Unique protein chains: 43
  • Unique nucleic acid chains: 4

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PRP8 isoform 12,413Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
SNU114 isoform 11,008Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
BRR2 isoform 12,163Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3E [auth d]101Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0014900.mRNA.1.CDS.1F [auth a],
Q [auth h]
196Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
SMD1 isoform 1G [auth b],
V [auth m]
146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0037700.mRNA.1.CDS.1H [auth c],
W [auth n]
110Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EI [auth e],
R [auth i]
94Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm protein FJ [auth f],
S [auth j]
86Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GK [auth g],
T [auth k]
77Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40204
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
HLJ1_G0053790.mRNA.1.CDS.1O [auth o]238Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0027490.mRNA.1.CDS.1P [auth p]111Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3U [auth l]81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
PRP9 isoform 1X [auth u]530Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP21Y [auth w]280Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P32524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
PRP11 isoform 1Z [auth v]266Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
HSH155 isoform 1AA [auth 1]971Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
HLJ1_G0043010.mRNA.1.CDS.1BA [auth 2]238Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
RSE1 isoform 1CA [auth 3]1,361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
HSH49 isoform 1DA [auth 4]213Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0056610.mRNA.1.CDS.1EA [auth 5]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
RDS3 complex subunit 10FA [auth 6]84Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0C074 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1GA [auth L]590Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q03654 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ03654
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Reference Sequence
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19HA [auth s],
IA [auth t],
JA [auth q],
KA [auth r]
503Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.3.2.27
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
SNT309 isoform 1LA [auth K]175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
BUD31 isoform 1MA [auth N]157Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
HLJ1_G0054350.mRNA.1.CDS.1NA [auth T]337Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45OA [auth P]379Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11PA [auth Q]364Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2QA [auth R]261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15RA [auth S]175Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q03772 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ03772
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Reference Sequence
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA leakage protein 1SA [auth Y]204Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q07930 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
SX2_G0027210.mRNA.1.CDS.1TA [auth X]128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC26UA [auth Z]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
CDC40 isoform 1VA [auth W]455Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21WA [auth U]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
CWC22 isoform 1XA [auth V]577Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC24YA [auth M]259Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
CWC27 isoform 1ZA [auth z]301Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPP2AB [auth y]185Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02521 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ02521
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Reference Sequence
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
CLF1 isoform 1BB [auth J]687Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
SYF1 isoform 1CB [auth I]859Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2DB [auth x]876Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for P20095 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP20095
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNA214Saccharomyces cerevisiae
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Reference Sequence
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Entity ID: 12
MoleculeChains LengthOrganismImage
U6 snRNAL [auth F]112Saccharomyces cerevisiae
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Reference Sequence
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Entity ID: 13
MoleculeChains LengthOrganismImage
pre-mRNAM [auth G]162Saccharomyces cerevisiae
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Reference Sequence
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Entity ID: 14
MoleculeChains LengthOrganismImage
U2 snRNAN [auth H]1,175Saccharomyces cerevisiae
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
(Subject of Investigation/LOI)

Query on IHP



Download:Ideal Coordinates CCD File
EB [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
(Subject of Investigation/LOI)

Query on GTP



Download:Ideal Coordinates CCD File
FB [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
AC [auth M]
BC [auth M]
MB [auth u]
NB [auth u]
OB [auth v]
AC [auth M],
BC [auth M],
MB [auth u],
NB [auth u],
OB [auth v],
QB [auth 5],
RB [auth 5],
SB [auth 5],
TB [auth N],
UB [auth N],
VB [auth N],
WB [auth Q],
XB [auth Q],
YB [auth R],
ZB [auth M]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
HB [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
GB [auth C]
IB [auth F]
JB [auth F]
KB [auth F]
LB [auth F]
GB [auth C],
IB [auth F],
JB [auth F],
KB [auth F],
LB [auth F],
PB [auth 3]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31930059

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references