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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



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
  • Structures With Same Primary Citation

  • 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, r ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
2413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 6
N
899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP6RNA6YBR055CYBR0508
Find proteins for P19735 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Spliceosomal protein DIB1
E
143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIB1CDH1SNU16YPR082CP9513.12
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
13 kDa ribonucleoprotein-associated protein
M
126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114
C
1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8
z
109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM8YJR022WJ1464YJR83.16
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
q
95Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM2SMX5SNP3YBL026WYBL0425
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3
r
89Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM3SMX4USS2YLR438C-A
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5
t
93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM5YER146W
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4
s
187Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM4SDB23USS1YER112W
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
O
587Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU66YOR308C05667
Find proteins for Q12420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
P, a, h
196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
Q, b, m
146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
R, c, n
110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
T, e, i
94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
U, f, j
86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing helicase BRR2
D
2163Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRR2RSS1SNU246YER172CSYGP-ORF66
EC: 3.6.4.13
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
U2 snRNP component HSH155
1
971Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HSH155YMR288WYM8021.14
Find proteins for P49955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RSE1
3
1361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSE1SAP130YML049CYM9827.03C
Find proteins for Q04693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RDS3
5
107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RDS3YPR094WP9513.2
Find proteins for Q06835 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
RDS3 complex subunit 10
6
85Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YSF3RCP10YNL138W-A
Find proteins for P0C074 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
U2 snRNP component IST3
X
148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IST3SNU17YIR005WYIB5W
Find proteins for P40565 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC26
Y
266Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD13CWC26SLC7YGL174WG1642
Find proteins for P46947 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA leakage protein 1
Z
204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PML1YLR016CL1591
Find proteins for Q07930 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
p
111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1YIR009WYIB9W
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP21
w
280Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP21SPP91YJL203WJ0322
Find proteins for P32524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP11
v
266Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP11PRP10RNA11YDL043CD2711
Find proteins for Q07350 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
23 kDa U4/U6.U5 small nuclear ribonucleoprotein component
W
194Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU23YDL098CD2378
Find proteins for Q12368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 38
0
242Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP38YGR075C
Find proteins for Q00723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SPP381
9
291Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPP381YBR152WYBR1202
Find proteins for P38282 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6
x
86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM6YDR378CD9481.18
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7
y
115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM7YNL147WN1202N1780
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
S, d, l
101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP4
K
465Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP4RNA4YPR178WP9705.6
Find proteins for P20053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
V, g, k
77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 31
L
494Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP31YGR091W
Find proteins for P49704 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Cold sensitive U2 snRNA suppressor 1
2
436Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CUS1YMR240CYM9408.02C
Find proteins for Q02554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Protein HSH49
4
213Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HSH49YOR319WO6142
Find proteins for Q99181 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
o
238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1YPL213W
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP9
u
530Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP9YDL030WD2773
Find proteins for P19736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP3
J
469Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP3RNA3YDR473CD8035.16
Find proteins for Q03338 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsLengthOrganism
U6 snRNAF112Saccharomyces cerevisiae S288C

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Entity ID: 17
MoleculeChainsLengthOrganism
U5 snRNAB214Saccharomyces cerevisiae S288C

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Entity ID: 26
MoleculeChainsLengthOrganism
U4 snRNAI161Saccharomyces cerevisiae S288C

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Entity ID: 28
MoleculeChainsLengthOrganism
Pre-mRNAG60Saccharomyces cerevisiae S288C

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Entity ID: 38
MoleculeChainsLengthOrganism
U2 snRNAH1175Saccharomyces cerevisiae S288C
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
MG
Query on MG

Download CCD File 
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

View Full Validation Report



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 

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