7V4T | pdb_00007v4t

Cryo-EM structure of Alphavirus M1

  • Classification: VIRUS
  • Organism(s): Alphavirus M1
  • Mutation(s): No 

  • Deposited: 2021-08-15 Released: 2022-08-17 
  • Deposition Author(s): Gao, Y., Jia, X., Zhang, Q.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7V4T

This is version 1.2 of the entry. See complete history. 

Literature

Cryo-EM evidence of viral N-glycosylation reveal receptor binding mechanisms of alphavirus M1

Song, D., Jia, X.

To be published.

Macromolecule Content 

  • Total Structure Weight: 499.23 kDa 
  • Atom Count: 31,508 
  • Modeled Residue Count: 4,080 
  • Deposited Residue Count: 4,508 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E1 glycoproteinA,
D [auth E],
G [auth I],
J [auth M]		438Alphavirus M1Mutation(s): 0 
UniProt
Find proteins for Q5Y388 (Getah virus)
Explore Q5Y388 
Go to UniProtKB:  Q5Y388
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5Y388
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
E2 glycoproteinB,
E [auth F],
H [auth J],
K [auth N]		422Alphavirus M1Mutation(s): 0 
UniProt
Find proteins for Q5Y388 (Getah virus)
Explore Q5Y388 
Go to UniProtKB:  Q5Y388
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5Y388
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid proteinC,
F [auth G],
I [auth K],
L [auth O]		267Alphavirus M1Mutation(s): 0 
UniProt
Find proteins for Q5Y388 (Getah virus)
Explore Q5Y388 
Go to UniProtKB:  Q5Y388
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5Y388
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG


Download:Ideal Coordinates CCD File
M [auth A]
N [auth B]
O [auth B]
P [auth E]
Q [auth F]
M [auth A],
N [auth B],
O [auth B],
P [auth E],
Q [auth F],
R [auth F],
S [auth I],
T [auth J],
U [auth J],
V [auth M],
W [auth N],
X [auth N]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONjspr

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81973342
National Natural Science Foundation of China (NSFC)China81773751
National Natural Science Foundation of China (NSFC)China81772675
National Natural Science Foundation of China (NSFC)China81903652
National Natural Science Foundation of China (NSFC)China81802536

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection