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- PDB-5ezq: Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural protein... -

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Basic information

Entry
Database: PDB / ID: 5ezq
TitleVenezuelan Equine Encephalitis Virus (VEEV) Nonstructural protein 2 (nsP2) Cysteine Protease
ComponentsNon-structural Protein 2 Cysteine Protease
KeywordsHYDROLASE / VEEV / nsP2 / Cysteine protease / alphavirus
Function / homology
Function and homology information


ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide adenylyltransferase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide adenylyltransferase / polynucleotide 5'-phosphatase 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 / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / GTP binding / host cell nucleus / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Alphavirus nsP2 protease domain / : / 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 ...Alphavirus nsP2 protease domain / : / 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-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral superfamily 1 RNA helicase core domain / Cathepsin B; Chain A / Vaccinia Virus protein VP39 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / 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 / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVenezuelan equine encephalitis virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsCompton, J.R. / Legler, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)CBCall4-CBM-05-2-0019 United States
CitationJournal: Biochemistry / Year: 2016
Title: Kinetic, Mutational, and Structural Studies of the Venezuelan Equine Encephalitis Virus Nonstructural Protein 2 Cysteine Protease.
Authors: Hu, X. / Compton, J.R. / Leary, D.H. / Olson, M.A. / Lee, M.S. / Cheung, J. / Ye, W. / Ferrer, M. / Southall, N. / Jadhav, A. / Morazzani, E.M. / Glass, P.J. / Marugan, J. / Legler, P.M.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural Protein 2 Cysteine Protease


Theoretical massNumber of molelcules
Total (without water)38,3421
Polymers38,3421
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15160 Å2
Unit cell
Length a, b, c (Å)60.805, 63.720, 86.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Non-structural Protein 2 Cysteine Protease


Mass: 38341.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cys-477 is partially oxidized.
Source: (gene. exp.) Venezuelan equine encephalitis virus (strain Trinidad donkey)
Strain: Trinidad donkey / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: P27282, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.44 % / Description: rod-shaped
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: JCSG+ Condition #15 (0.1 M Bicine pH 8.5, 20% PEG 6000)

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jan 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.66→63.72 Å / Num. obs: 40129 / % possible obs: 99.6 % / Redundancy: 6.01 % / Rsym value: 0.0406 / Net I/σ(I): 21.91
Reflection shellResolution: 1.66→1.76 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.3751 / Mean I/σ(I) obs: 3.24 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hwk

2hwk


Resolution: 1.66→51.21 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21088 1941 4.9 %RANDOM
Rwork0.20229 ---
obs0.20271 38017 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.608 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0 Å20 Å2
2--0.83 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.66→51.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 0 212 2770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192810
X-RAY DIFFRACTIONr_bond_other_d00.022674
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9553839
X-RAY DIFFRACTIONr_angle_other_deg3.65136167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8675359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55823.182132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7915486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5851524
X-RAY DIFFRACTIONr_chiral_restr0.0710.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213281
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02685
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7461.5691376
X-RAY DIFFRACTIONr_mcbond_other0.7451.5671375
X-RAY DIFFRACTIONr_mcangle_it1.3562.3491752
X-RAY DIFFRACTIONr_mcangle_other1.3562.3511753
X-RAY DIFFRACTIONr_scbond_it0.6781.6851434
X-RAY DIFFRACTIONr_scbond_other0.6781.6851434
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2022.4852087
X-RAY DIFFRACTIONr_long_range_B_refined3.43112.6953260
X-RAY DIFFRACTIONr_long_range_B_other3.17812.4233175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 139 -
Rwork0.318 2664 -
obs--95.57 %

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