7DCO

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


This is version 1.0 of the entry. See complete history


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: 10.1126/science.abe8863
  • Primary Citation of Related Structures:  
    7DCP, 7DCQ, 7DCO, 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 ...

    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

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PRP8 isoform 1A2413Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SNU114 isoform 1C1008Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SCNYR20_0010004500SCP684_0010004600
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Find proteins for A0A6A5PW35 (Saccharomyces cerevisiae)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
BRR2 isoform 1D2163Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3E [auth d]101Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4325PACBIOSEQ_LOCUS4365SCNYR20_0004018800SCP684_0004018500
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
BJ4_G0014900.mRNA.1.CDS.1F [auth a], Q [auth h]196Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS1974PACBIOSEQ_LOCUS2014SCNYR20_0011009900SCP684_0011009300
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
SMD1 isoform 1G [auth b], V [auth m]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
BJ4_G0037700.mRNA.1.CDS.1H [auth c], W [auth n]110Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4474PACBIOSEQ_LOCUS4533
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EI [auth e], R [auth i]94Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS6005PACBIOSEQ_LOCUS6094SCNYR20_0002028400SCP684_0003027800
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Sm protein FJ [auth f], S [auth j]86Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS6776SCNYR20_0005040600SCP684_0005040000
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Entity ID: 11
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Small nuclear ribonucleoprotein GK [auth g], T [auth k]77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
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Entity ID: 15
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HLJ1_G0053790.mRNA.1.CDS.1O [auth o]238Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS6349
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Entity ID: 16
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BJ4_G0027490.mRNA.1.CDS.1P [auth p]111Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS1835
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Find proteins for A0A6A5Q318 (Saccharomyces cerevisiae)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3U [auth l]81Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4325PACBIOSEQ_LOCUS4365SCNYR20_0004018800SCP684_0004018500
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
PRP9 isoform 1X [auth u]530Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP21Y [auth w]280Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP21SPP91YJL203WJ0322
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Entity ID: 20
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PRP11 isoform 1Z [auth v]266Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
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HSH155 isoform 1AA [auth 1]971Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
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HLJ1_G0043010.mRNA.1.CDS.1BA [auth 2]238Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS5100
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Entity ID: 23
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RSE1 isoform 1CA [auth 3]1361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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HSH49 isoform 1DA [auth 4]213Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
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BJ4_G0056610.mRNA.1.CDS.1EA [auth 5]107Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS6668PACBIOSEQ_LOCUS6762
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
RDS3 complex subunit 10FA [auth 6]84Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YSF3RCP10YNL138W-A
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1GA [auth L]590Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1NTC85YMR213WYM8261.07
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Entity ID: 28
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Pre-mRNA-processing factor 19JA [auth q], KA [auth r], HA [auth s], IA [auth t]503Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.3.2.27
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Entity ID: 29
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SNT309 isoform 1LA [auth K]175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
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BUD31 isoform 1MA [auth N]157Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS715SCNYR20_0014010200
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
HLJ1_G0054350.mRNA.1.CDS.1NA [auth T]337Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS6409SCNYR20_0005011300SCP684_0005011600
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Entity ID: 32
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Pre-mRNA-processing protein 45OA [auth P]379Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
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Pre-mRNA-splicing factor SLT11PA [auth Q]364Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2QA [auth R]261Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS800SCNYR20_0001003200SCP684_0001003100
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15RA [auth S]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15YDR163WYD8358.17
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA leakage protein 1SA [auth Y]204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PML1YLR016CL1591
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
SX2_G0027210.mRNA.1.CDS.1TA [auth X]128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
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Pre-mRNA-splicing factor CWC26UA [auth Z]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
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CDC40 isoform 1VA [auth W]455Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
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Pre-mRNA-splicing factor CWC21WA [auth U]135Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS1518
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Entity ID: 41
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CWC22 isoform 1XA [auth V]577Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
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Pre-mRNA-splicing factor CWC24YA [auth M]259Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4522PACBIOSEQ_LOCUS4587SCNYR20_0004032800SCP684_0004032400
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Entity ID: 43
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CWC27 isoform 1ZA [auth z]301Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
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Pre-mRNA-splicing factor SPP2AB [auth y]185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPP2YOR148C
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
CLF1 isoform 1BB [auth J]687Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SCNYR20_0004016200SCP684_0004015900
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Find proteins for A0A6A5PT67 (Saccharomyces cerevisiae)
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
SYF1 isoform 1CB [auth I]859Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2DB [auth x]876Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP2RNA2YNR011CN2048
EC: 3.6.4.13
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNAB214Saccharomyces cerevisiae
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Entity ID: 12
MoleculeChainsLengthOrganismImage
U6 snRNAL [auth F]112Saccharomyces cerevisiae
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Entity ID: 13
MoleculeChainsLengthOrganismImage
pre-mRNAM [auth G]162Saccharomyces cerevisiae
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Entity ID: 14
MoleculeChainsLengthOrganismImage
U2 snRNAN [auth H]1175Saccharomyces cerevisiae
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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EB [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP
Query on GTP

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FB [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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AC [auth M] , BC [auth M] , MB [auth u] , NB [auth u] , OB [auth v] , QB [auth 5] , RB [auth 5] , SB [auth 5] , 
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
 Ligand Interaction
CA
Query on CA

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HB [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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GB [auth C], IB [auth F], JB [auth F], KB [auth F], LB [auth F], PB [auth 3]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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