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- PDB-43of: Cryo-EM structure of a virus helcal scaffolds -

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Basic information

Entry
Database: PDB / ID: 43of
TitleCryo-EM structure of a virus helcal scaffolds
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / Virus ring scaffold / Circular scaffold / Macromolecular ring complex
Function / homology
Function and homology information


host cell filopodium / mRNA methyltransferase activity / polynucleotide adenylyltransferase / mRNA 5'-phosphatase / mRNA 5'-triphosphate monophosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity ...host cell filopodium / mRNA methyltransferase activity / polynucleotide adenylyltransferase / mRNA 5'-phosphatase / mRNA 5'-triphosphate monophosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / ribonucleoside triphosphate phosphatase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / RNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / DNA-templated transcription / GTP binding / host cell cytoplasm / host cell plasma membrane / host cell nucleus / metal ion binding / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
: / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase ...: / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Viral superfamily 1 RNA helicase core domain / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesVenezuelan equine encephalitis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsZhang, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem Biophys Res Commun / Year: 2026
Title: Cryo-EM reveals a C15 annular stacking assembly of the VEEV nsP3 Alphavirus Unique Domain.
Authors: Rong Wang / Qiulan Wu / Qiaoshuo Zhang / Kuo Zhang /
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 ...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.
History
DepositionJul 10, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 28, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 3
B: Non-structural protein 3
C: Non-structural protein 3
D: Non-structural protein 3
E: Non-structural protein 3
F: Non-structural protein 3
G: Non-structural protein 3
H: Non-structural protein 3
I: Non-structural protein 3
J: Non-structural protein 3
K: Non-structural protein 3
L: Non-structural protein 3
M: Non-structural protein 3
N: Non-structural protein 3
O: Non-structural protein 3
P: Non-structural protein 3
Q: Non-structural protein 3
R: Non-structural protein 3
S: Non-structural protein 3
T: Non-structural protein 3
U: Non-structural protein 3
V: Non-structural protein 3
W: Non-structural protein 3
X: Non-structural protein 3
Y: Non-structural protein 3
Z: Non-structural protein 3
a: Non-structural protein 3
b: Non-structural protein 3
c: Non-structural protein 3
d: Non-structural protein 3
e: Non-structural protein 3
f: Non-structural protein 3
g: Non-structural protein 3
h: Non-structural protein 3
i: Non-structural protein 3
j: Non-structural protein 3
k: Non-structural protein 3
l: Non-structural protein 3
m: Non-structural protein 3
n: Non-structural protein 3
o: Non-structural protein 3
p: Non-structural protein 3
q: Non-structural protein 3
r: Non-structural protein 3
s: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)684,66990
Polymers681,72545
Non-polymers2,94345
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Non-structural protein 3 / nsP3


Mass: 15149.452 Da / Num. of mol.: 45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus (strain Trinidad donkey)
Production host: Homo sapiens (human)
References: UniProt: P27282, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: non-structure protein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Venezuelan equine encephalitis virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32509 / Symmetry type: POINT
RefinementHighest resolution: 3.54 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00448060
ELECTRON MICROSCOPYf_angle_d0.60265070
ELECTRON MICROSCOPYf_dihedral_angle_d4.7956570
ELECTRON MICROSCOPYf_chiral_restr0.0447425
ELECTRON MICROSCOPYf_plane_restr0.0058325

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