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- EMDB-82032: Cryo-EM structure of a virus helcal scaffolds -

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Basic information

Entry
Database: EMDB / ID: EMD-82032
TitleCryo-EM structure of a virus helcal scaffolds
Map data
Sample
  • Complex: non-structure protein
    • Protein or peptide: Non-structural protein 3
  • Ligand: ZINC ION
KeywordsVirus ring scaffold / Circular scaffold / Macromolecular ring complex / VIRAL PROTEIN
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 / Venezuelan equine encephalitis virus (strain Trinidad donkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsZhang K
Funding support1 items
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, 2026-
Header (metadata) releaseOct 28, 2026-
Map releaseOct 28, 2026-
UpdateOct 28, 2026-
Current statusOct 28, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_82032.png

Downloads & links

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Map

FileDownload / File: emd_82032.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.86 Å/pix.
x 480 pix.
= 410.4 Å		0.86 Å/pix.
x 480 pix.
= 410.4 Å		0.86 Å/pix.
x 480 pix.
= 410.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-17.175218999999998 - 23.389749999999999
Average (Standard dev.)0.000000000001742 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 410.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_82032_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_82032_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : non-structure protein

EntireName: non-structure protein
Components
  • Complex: non-structure protein
    • Protein or peptide: Non-structural protein 3
  • Ligand: ZINC ION

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Supramolecule #1: non-structure protein

SupramoleculeName: non-structure protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Venezuelan equine encephalitis virus

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Macromolecule #1: Non-structural protein 3

MacromoleculeName: Non-structural protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 45 / Enantiomer: LEVO
EC number: Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
Source (natural)Organism: Venezuelan equine encephalitis virus (strain Trinidad donkey)
Molecular weightTheoretical: 15.149452 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ELVRVHPKSS LAGRKGYSTS DGKTFSYLEG TKFHQAAKDI AEINAMWPVA TEANEQVCMY ILGESMSSIR SKCPVEESEA STPPSTLPC LCIHAMTPER VQRLKASRPE QITVCSSFPL PKYRITGVQK IQCSQPIL

UniProtKB: Polyprotein P1234

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 45 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 32509
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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