5ZWO

Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structures of the fully assembledSaccharomyces cerevisiaespliceosome before activation

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

(2018) Science 360: 1423-1429

  • DOI: 10.1126/science.aau0325
  • Primary Citation of Related Structures:  
    5ZWM, 5ZWN, 5ZWO

  • PubMed Abstract: 
  • The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the Saccharomyces cerevisiae pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively ...

    The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the Saccharomyces cerevisiae pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon-5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.


    Organizational Affiliation

    Institute of Biology, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou 310064, Zhejiang Province, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8A2413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP4B [auth K]465Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP4RNA4YPR178WP9705.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 31C [auth L]494Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP31YGR091W
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 6D [auth N]899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP6RNA6YBR055CYBR0508
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP3E [auth J]469Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP3RNA3YDR473CD8035.16
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosomal protein DIB1F [auth E]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIB1CDH1SNU16YPR082CP9513.12
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinG [auth M]126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
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Entity ID: 8
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Pre-mRNA-splicing factor SNU114H [auth C]1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8I [auth z]109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM8YJR022WJ1464YJR83.16
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2J [auth q]95Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM2SMX5SNP3YBL026WYBL0425
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3K [auth r]89Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM3SMX4USS2YLR438C-A
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Entity ID: 12
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U6 snRNA-associated Sm-like protein LSm6L [auth x]86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM6YDR378CD9481.18
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Entity ID: 13
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U6 snRNA-associated Sm-like protein LSm5M [auth t]93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM5YER146W
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7N [auth y]115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM7YNL147WN1202N1780
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4O [auth s]187Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM4SDB23USS1YER112W
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
66 kDa U4/U6.U5 small nuclear ribonucleoprotein componentR [auth O]587Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU66YOR308C05667
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3EA [auth S],
S [auth d],
XA [auth l]
101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BBA [auth P],
T [auth a],
TA [auth h]
196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1CA [auth Q],
U [auth b],
YA [auth m]
146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2DA [auth R],
V [auth c],
ZA [auth n]
110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EFA [auth T],
W [auth e],
UA [auth i]
94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FGA [auth U],
X [auth f],
VA [auth j]
86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GHA [auth V],
Y [auth g],
WA [auth k]
77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
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Entity ID: 27
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Pre-mRNA-splicing helicase BRR2AA [auth D]2163Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRR2RSS1SNU246YER172CSYGP-ORF66
EC: 3.6.4.13
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Entity ID: 29
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U2 snRNP component HSH155JA [auth 1]971Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HSH155YMR288WYM8021.14
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Cold sensitive U2 snRNA suppressor 1KA [auth 2]436Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CUS1YMR240CYM9408.02C
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Entity ID: 31
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Pre-mRNA-splicing factor RSE1LA [auth 3]1361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSE1SAP130YML049CYM9827.03C
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Entity ID: 32
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Protein HSH49MA [auth 4]213Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HSH49YOR319WO6142
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Entity ID: 33
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Pre-mRNA-splicing factor RDS3NA [auth 5]107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RDS3YPR094WP9513.2
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RDS3 complex subunit 10OA [auth 6]85Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YSF3RCP10YNL138W-A
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U2 snRNP component IST3PA [auth X]148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IST3SNU17YIR005WYIB5W
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Pre-mRNA-splicing factor CWC26QA [auth Y]266Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD13CWC26SLC7YGL174WG1642
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Pre-mRNA leakage protein 1RA [auth Z]204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PML1YLR016CL1591
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Entity ID: 39
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U2 small nuclear ribonucleoprotein A'AB [auth o]238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1YPL213W
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U2 small nuclear ribonucleoprotein B''BB [auth p]111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1YIR009WYIB9W
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Pre-mRNA-splicing factor PRP9CB [auth u]530Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP9YDL030WD2773
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Pre-mRNA-splicing factor PRP21DB [auth w]280Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP21SPP91YJL203WJ0322
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Pre-mRNA-splicing factor PRP11EB [auth v]266Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP11PRP10RNA11YDL043CD2711
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23 kDa U4/U6.U5 small nuclear ribonucleoprotein componentFB [auth W]194Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU23YDL098CD2378
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Pre-mRNA-splicing factor 38GB [auth 0]242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP38YGR075C
UniProt
Find proteins for Q00723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q00723
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UniProt GroupQ00723
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPP381HB [auth 9]291Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPP381YBR152WYBR1202
UniProt
Find proteins for P38282 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38282 
Go to UniProtKB:  P38282
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UniProt GroupP38282
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Entity ID: 16
MoleculeChainsLengthOrganismImage
U6 snRNAP [auth F]112Saccharomyces cerevisiae S288C
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Entity ID: 17
MoleculeChainsLengthOrganismImage
U5 snRNAQ [auth B]214Saccharomyces cerevisiae S288C
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Entity ID: 26
MoleculeChainsLengthOrganismImage
U4 snRNAZ [auth I]161Saccharomyces cerevisiae S288C
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Entity ID: 28
MoleculeChainsLengthOrganismImage
Pre-mRNAIA [auth G]60Saccharomyces cerevisiae S288C
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Entity ID: 38
MoleculeChainsLengthOrganismImage
U2 snRNASA [auth H]1175Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

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JB [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31430020
National Natural Science Foundation of ChinaChina31621092
Ministry of Science and Technology (China)China2016YFA0501100

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release