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- PDB-5gjc: Zika virus NS3 helicase in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 5gjc
TitleZika virus NS3 helicase in complex with ATP
ComponentsNS3 helicase
KeywordsHYDROLASE / zika virus / helicase / ATP / Mn ion
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsTian, H.L. / Ji, X.Y. / Yang, X.Y. / Zhang, Z.X. / Lu, Z.K. / Yang, K.L. / Chen, C. / Zhao, Q. / Chi, H. / Mu, Z.Y. ...Tian, H.L. / Ji, X.Y. / Yang, X.Y. / Zhang, Z.X. / Lu, Z.K. / Yang, K.L. / Chen, C. / Zhao, Q. / Chi, H. / Mu, Z.Y. / Xie, W. / Wang, Z.F. / Lou, H.Q. / Yang, H.T. / Rao, Z.H.
CitationJournal: Protein Cell / Year: 2016
Title: Structural basis of Zika virus helicase in recognizing its substrates
Authors: Tian, H.L. / Ji, X.Y. / Yang, X.Y. / Zhang, Z.X. / Lu, Z.K. / Yang, K.L. / Chen, C. / Zhao, Q. / Chi, H. / Mu, Z.Y. / Xie, W. / Wang, Z.F. / Lou, H.Q. / Yang, H.T. / Rao, Z.H.
History
DepositionJun 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)50,1983
Polymers49,6361
Non-polymers5622
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-9 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.595, 74.167, 57.740
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NS3 helicase


Mass: 49635.598 Da / Num. of mol.: 1 / Fragment: UNP residues 1682-2119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A142DS38, UniProt: A0A0U4DG08*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.4
Details: 0.1M HEPES(pH 7.4), 9% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 42724 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.8
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.942

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JMT

5jmt


Resolution: 2.204→37.729 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.12
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2474 2043 4.78 %
Rwork0.197 --
obs0.1995 42723 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.204→37.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 32 107 3535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043502
X-RAY DIFFRACTIONf_angle_d0.9144750
X-RAY DIFFRACTIONf_dihedral_angle_d15.9161315
X-RAY DIFFRACTIONf_chiral_restr0.032524
X-RAY DIFFRACTIONf_plane_restr0.004609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2044-2.25570.38421310.28392607X-RAY DIFFRACTION94
2.2557-2.31210.30471480.26772733X-RAY DIFFRACTION100
2.3121-2.37460.3142990.2452724X-RAY DIFFRACTION100
2.3746-2.44450.28851190.23922758X-RAY DIFFRACTION100
2.4445-2.52330.23071230.22132687X-RAY DIFFRACTION97
2.5233-2.61350.2771190.22372762X-RAY DIFFRACTION100
2.6135-2.71810.30121540.23282693X-RAY DIFFRACTION99
2.7181-2.84180.29121190.21942753X-RAY DIFFRACTION100
2.8418-2.99150.2891410.22082722X-RAY DIFFRACTION100
2.9915-3.17890.28051490.21822746X-RAY DIFFRACTION100
3.1789-3.42420.2371580.21262690X-RAY DIFFRACTION99
3.4242-3.76850.2251440.19212725X-RAY DIFFRACTION100
3.7685-4.31310.24881710.17672708X-RAY DIFFRACTION100
4.3131-5.43150.21461380.16842675X-RAY DIFFRACTION98
5.4315-37.73440.21371300.16992697X-RAY DIFFRACTION98

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