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- PDB-8duf: Crystal structure of Venezuelan Equine Encephalitis alphavirus (V... -

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Basic information

Entry
Database: PDB / ID: 8duf
TitleCrystal structure of Venezuelan Equine Encephalitis alphavirus (VEEV) nonstructural protein 2 (nsp2) (K741A/K767A) protease domain
Componentsnsp2 protease domain
KeywordsVIRAL PROTEIN / nonstructural protein / protease
Function / homology
Function and homology information


: / host cell filopodium / mRNA methyltransferase activity / polynucleotide 5'-phosphatase activity / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane ...: / host cell filopodium / mRNA methyltransferase activity / polynucleotide 5'-phosphatase activity / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / RNA helicase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / proteolysis / RNA binding / ATP binding / plasma membrane
Similarity search - Function
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 ...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 speciesVenezuelan equine encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsLountos, G.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Mol.Biol. / Year: 2023
Title: Self-inhibited State of Venezuelan Equine Encephalitis Virus (VEEV) nsP2 Cysteine Protease: A Crystallographic and Molecular Dynamics Analysis.
Authors: Hoffka, G. / Lountos, G.T. / Needle, D. / Wlodawer, A. / Waugh, D.S. / Tozser, J. / Motyan, J.A.
History
DepositionJul 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nsp2 protease domain


Theoretical massNumber of molelcules
Total (without water)36,5471
Polymers36,5471
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14260 Å2
Unit cell
Length a, b, c (Å)45.186, 46.165, 175.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein nsp2 protease domain / Non-structural polyprotein


Mass: 36546.684 Da / Num. of mol.: 1 / Mutation: K1276A/K1302A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus / Gene: NSP, WQI_35787gpNSP, WQI_36543gpNSP / Plasmid: pDN2164 / Production host: Escherichia coli (E. coli) / References: UniProt: M1KSA0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M sodium formate, 10% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 64078 / % possible obs: 98.6 % / Redundancy: 5.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.039 / Net I/σ(I): 31.7
Reflection shellResolution: 1.46→1.49 Å / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 2 / Num. unique obs: 3040 / CC1/2: 0.545 / Rpim(I) all: 0.662

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HWK

2hwk


Resolution: 1.46→40.194 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 3182 4.97 %
Rwork0.1535 60785 -
obs0.1556 63967 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.31 Å2 / Biso mean: 23.3096 Å2 / Biso min: 8.82 Å2
Refinement stepCycle: final / Resolution: 1.46→40.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 0 326 2767
Biso mean---37.93 -
Num. residues----308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.46-1.48170.29391050.1896233089
1.4817-1.50480.25271360.1853259396
1.5048-1.52950.241290.1799252497
1.5295-1.55590.21821600.1656257297
1.5559-1.58410.18731330.1544261599
1.5841-1.61460.24391600.1485258298
1.6146-1.64760.17871410.1422258198
1.6476-1.68340.18121010.1379266099
1.6834-1.72260.19641530.1384260899
1.7226-1.76560.21571400.1367262699
1.7656-1.81340.20671610.1422263399
1.8134-1.86670.18411470.1411263099
1.8667-1.9270.17671330.13252659100
1.927-1.99590.19981560.142652100
1.9959-2.07580.16311200.13482708100
2.0758-2.17020.18581380.1362672100
2.1702-2.28460.18681280.13992709100
2.2846-2.42780.16561260.14042718100
2.4278-2.61520.17631350.15782691100
2.6152-2.87830.18041460.16352734100
2.8783-3.29460.21031330.16542752100
3.2946-4.15020.19011530.1479275499
4.1502-40.10.22531480.1785278295

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