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 43OF | pdb_000043of

Cryo-EM structure of a virus helcal scaffolds


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 43OF

This is version 1.0 of the entry. See complete history. 

Literature

Cryo-EM reveals a C15 annular stacking assembly of the VEEV nsP3 Alphavirus Unique Domain.

Wang, R., Wu, Q., Zhang, Q., Zhang, K.

(2026) Biochem Biophys Res Commun 839: 154736-154736

  • DOI: https://doi.org/10.1016/j.bbrc.2026.154736
  • Primary Citation Related Structures: 
    43OF

  • PubMed Abstract: 

    Alphaviruses are arthropod-borne pathogens that cause significant human disease, including severe arthritis and encephalitis. Among the four nonstructural proteins (nsP1-nsP4) that form the viral replication complex (RC), nsP3 is the least functionally characterized. Recent studies have shown that CHIKV-nsP3 forms a right-handed helical scaffold, while Venezuelan equine encephalitis virus (VEEV) nsP3 forms gel-like biomolecular condensates mediated by its Alphavirus Unique Domain (AUD). In this study, we used cryo-electron microscopy to reveal a closed annular stacking assembly of VEEV-nsP3, composed of C15-symmetric rings that stack axially without helical offset-fundamentally differing from the helical arrangement of CHIKV. Structural comparisons demonstrate that this divergence arises from the loss of three key hydrogen bond networks, particularly an axial hydrogen bond that drives helical propagation in CHIKV but is uniquely absent in VEEV. Furthermore, we propose that the proteolytic cleavage at the nsP2/nsP3 junction regulates the annular to tubular transition. Our work provides insights into the structural diversity and dynamic regulation of alphavirus RC crown formation, with implications for understanding replication complex assembly across this viral lineage.


  • Organizational Affiliation: 
    • Department of Gastrointestinal Surgery, Shenzhen People's Hospital, The Second Clinic Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China.

Macromolecule Content 

  • Total Structure Weight: 684.67 kDa 
  • Atom Count: 47,115 
  • Modeled Residue Count: 6,120 
  • Deposited Residue Count: 6,165 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-structural protein 3137Venezuelan equine encephalitis virus (strain Trinidad donkey)Mutation(s): 0 
EC: 3.2.2
UniProt
Find proteins for P27282 (Venezuelan equine encephalitis virus (strain Trinidad donkey))
Explore P27282 
Go to UniProtKB:  P27282
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27282
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AB [auth H]
AC [auth h]
BB [auth I]
BC [auth i]
CB [auth J]
AB [auth H],
AC [auth h],
BB [auth I],
BC [auth i],
CB [auth J],
CC [auth j],
DB [auth K],
DC [auth k],
EB [auth L],
EC [auth l],
FB [auth M],
FC [auth m],
GB [auth N],
GC [auth n],
HB [auth O],
HC [auth o],
IB [auth P],
IC [auth p],
JB [auth Q],
JC [auth q],
KB [auth R],
KC [auth r],
LB [auth S],
LC [auth s],
MB [auth T],
NB [auth U],
OB [auth V],
PB [auth W],
QB [auth X],
RB [auth Y],
SB [auth Z],
TA [auth A],
TB [auth a],
UA [auth B],
UB [auth b],
VA [auth C],
VB [auth c],
WA [auth D],
WB [auth d],
XA [auth E],
XB [auth e],
YA [auth F],
YB [auth f],
ZA [auth G],
ZB [auth g]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-10-28 
  • Deposition Author(s): Zhang, K.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-28
    Type: Initial release