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- PDB-8pk7: Helical reconstruction of CHIKV nsP3 helical scaffolds -

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Basic information

Entry
Database: PDB / ID: 8pk7
TitleHelical reconstruction of CHIKV nsP3 helical scaffolds
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / Helical scaffold / Replication complex / Alpha granules / Viral factories
Function / homology
Function and homology information


host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
: / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase ...: / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesChikungunya virus strain S27-African prototype
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsReguera, J. / Hons, M. / Zimberger, C. / Ptchelkine, D. / Jones, R. / Desfosses, A.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0023-01 France
ATIP-Avenir2015 France
CitationJournal: To Be Published
Title: The alphavirus nsP3 protein forms helical tubular scaffolds important for viral replication and particle assembly
Authors: Reguera, J. / Hons, M. / Zimberger, C. / Ptchelkine, D. / Jones, R. / Desfosses, A.
History
DepositionJun 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4842
Polymers57,4181
Non-polymers651
Water00
1
A: Non-structural protein 3
hetero molecules

A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
hetero molecules

A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
hetero molecules

A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
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A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,046,632106
Polymers3,043,16553
Non-polymers3,46753
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation52

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Components

#1: Protein Non-structural protein 3 / nsP3


Mass: 57418.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus strain S27-African prototype
Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8JUX6, ADP-ribose 1''-phosphate phosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical scaffold assembly of CHIKV nsP3 mediated by its Unique alphavirus domain.
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 220.25 kDa/nm / Experimental value: NO
Source (natural)Organism: Chikungunya virus strain S27-African prototype
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: his sample was heterogeneous in lenght
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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: 800 nm
Image recordingElectron dose: 18.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
4cryoSPARCCTF correction
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -164.175 ° / Axial rise/subunit: 2.782 Å / Axial symmetry: C1
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 807973
Details: The assembly was calculated from the helical reconstruction of nsP3 from PDB 8PHZ subunit A. This was refined on a local refinement map at 2.35 A resolution
Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 8PHZ

8phz


Pdb chain-ID: A / Accession code: 8PHZ / Chain residue range: 174-600 / Pdb chain residue range: 174-600 / Source name: PDB / Type: experimental model

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