5ZWN

Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 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


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein 70 kDa homolog
Q
300Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNP1
Find proteins for Q00916 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q00916
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein C
R
231Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: YHC1
Find proteins for Q05900 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05900
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A
S
298Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MUD1
Find proteins for P32605 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32605
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein component PRP42
T
544Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP42 (MUD16, SNU65)
Find proteins for Q03776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03776
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 39
U
629Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP39
Find proteins for P39682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39682
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Protein NAM8
V
523Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NAM8 (MRE2)
Find proteins for Q00539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q00539
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
56 kDa U1 small nuclear ribonucleoprotein component
W
492Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU56 (MUD10)
Find proteins for Q03782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03782
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
a
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMB1
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
b
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD1
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02260
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
c
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
d
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD3
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43321
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SME1
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX3
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54999
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX2 (SNP2)
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40204
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein component SNU71
X
619Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU71
Find proteins for P53207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53207
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Protein LUC7
Y
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LUC7 (EPE1, EXM2)
Find proteins for Q07508 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07508
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
U1 snRNP
x
49N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing ATP-dependent RNA helicase PRP28
y
588Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP28
EC: 3.6.4.13
Find proteins for P23394 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23394
Entity ID: 1
MoleculeChainsLengthOrganism
pre-mRNAG22Saccharomyces cerevisiae S288C
Entity ID: 2
MoleculeChainsLengthOrganism
U1 snRNAP568Saccharomyces cerevisiae S288C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
R, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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