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- PDB-5jwh: Apo structure -

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Basic information

Entry
Database: PDB / ID: 5jwh
TitleApo structure
ComponentsNS3 helicase
KeywordsHYDROLASE / NTPase / helicase
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / serine-type endopeptidase activity ...ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCao, X. / Li, Y. / Jin, T.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Molecular mechanism of divalent-metal-induced activation of NS3 helicase and insights into Zika virus inhibitor design.
Authors: Cao, X. / Li, Y. / Jin, X. / Li, Y. / Guo, F. / Jin, T.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS3 helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4942
Polymers51,4321
Non-polymers621
Water8,863492
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.290, 52.600, 65.110
Angle α, β, γ (deg.)90.00, 105.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NS3 helicase


Mass: 51431.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A146CJG7*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.03 Å3/Da / Density % sol: 39.54 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 8000, 5% MPD, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 157613 / % possible obs: 98.8 % / Redundancy: 6.89 % / CC1/2: 0.998 / Net I/σ(I): 15.92
Reflection shellResolution: 1.4→1.49 Å / Redundancy: 6.07 % / Mean I/σ(I) obs: 1.81 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WZQ

2wzq


Resolution: 1.4→31.433 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.5
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2127 3934 2.5 %
Rwork0.1781 --
obs0.179 157613 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→31.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 4 492 3965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083643
X-RAY DIFFRACTIONf_angle_d0.9634960
X-RAY DIFFRACTIONf_dihedral_angle_d22.7341397
X-RAY DIFFRACTIONf_chiral_restr0.087554
X-RAY DIFFRACTIONf_plane_restr0.007644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4002-1.41730.35921290.33534798X-RAY DIFFRACTION86
1.4173-1.43520.29211270.32165120X-RAY DIFFRACTION93
1.4352-1.45410.36341250.29985427X-RAY DIFFRACTION97
1.4541-1.4740.3171480.28925584X-RAY DIFFRACTION100
1.474-1.49510.29831290.2775574X-RAY DIFFRACTION100
1.4951-1.51740.29431400.26415514X-RAY DIFFRACTION100
1.5174-1.54110.26171500.23795599X-RAY DIFFRACTION100
1.5411-1.56640.25011270.22485516X-RAY DIFFRACTION100
1.5664-1.59340.27251470.21685663X-RAY DIFFRACTION100
1.5934-1.62240.26681420.20935486X-RAY DIFFRACTION100
1.6224-1.65360.21871490.20265545X-RAY DIFFRACTION100
1.6536-1.68730.24231330.19875536X-RAY DIFFRACTION100
1.6873-1.7240.23311470.1885582X-RAY DIFFRACTION100
1.724-1.76410.20731390.19285555X-RAY DIFFRACTION100
1.7641-1.80820.23161460.18955623X-RAY DIFFRACTION100
1.8082-1.85710.27451410.19215521X-RAY DIFFRACTION100
1.8571-1.91180.2431400.18665563X-RAY DIFFRACTION100
1.9118-1.97340.2161430.17665512X-RAY DIFFRACTION100
1.9734-2.0440.21851450.17985632X-RAY DIFFRACTION100
2.044-2.12580.18171420.17525495X-RAY DIFFRACTION100
2.1258-2.22250.22821430.17285566X-RAY DIFFRACTION100
2.2225-2.33970.22221390.17365550X-RAY DIFFRACTION100
2.3397-2.48620.25391500.17015573X-RAY DIFFRACTION100
2.4862-2.6780.17771360.17265541X-RAY DIFFRACTION100
2.678-2.94740.20391540.17245554X-RAY DIFFRACTION100
2.9474-3.37340.1931450.16015542X-RAY DIFFRACTION100
3.3734-4.24850.16721430.14185529X-RAY DIFFRACTION99
4.2485-31.44050.19421350.16414979X-RAY DIFFRACTION90

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