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- PDB-7v4r: The crystal structure of KFDV NS3H bound with Pi -

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Basic information

Entry
Database: PDB / ID: 7v4r
TitleThe crystal structure of KFDV NS3H bound with Pi
ComponentsSerine protease NS3
KeywordsHYDROLASE / KFDV / NS3 helicase / NTPase / Pi
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C ...Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / 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, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like 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 / 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
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesKyasanur forest disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, C.Y. / Jin, T.C.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Kyasanur Forest disease virus NS3 helicase: Insights into structure, activity, and inhibitors.
Authors: Zhang, C. / Li, Y. / Samad, A. / He, H. / Ma, H. / Chen, Y. / Jin, T.
History
DepositionAug 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5225
Polymers50,1791
Non-polymers3444
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-26 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.537, 53.091, 189.843
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 Serine protease NS3 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 50178.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kyasanur forest disease virus / Production host: Escherichia coli (E. coli)
References: UniProt: D7RF80, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 800 mM K2HPO4, 800 mM Na3PO4, 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.1→47.46 Å / Num. obs: 26233 / % possible obs: 98.5 % / Redundancy: 23.5 % / CC1/2: 0.999 / Rrim(I) all: 0.132 / Net I/σ(I): 22.48
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 19.4 % / Mean I/σ(I) obs: 2.48 / Num. unique obs: 3860 / CC1/2: 0.74 / Rrim(I) all: 128.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JNO

7jno


Resolution: 2.1→47.46 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 4860 9.98 %
Rwork0.2235 43855 -
obs0.227 26180 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.09 Å2 / Biso mean: 47.0221 Å2 / Biso min: 21.48 Å2
Refinement stepCycle: final / Resolution: 2.1→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 16 45 3523
Biso mean--74.19 39.8 -
Num. residues----437
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.130.3381000.365894062
2.13-2.150.32771600.3148142295
2.15-2.180.3321620.29821465100
2.18-2.20.33161690.2871490100
2.2-2.230.38761630.2937142599
2.23-2.260.33231680.308149899
2.26-2.30.32611760.27111530100
2.3-2.330.2911550.27651412100
2.33-2.370.31831740.25621516100
2.37-2.410.29311660.27211473100
2.41-2.450.30921630.25981470100
2.45-2.490.311710.25771489100
2.49-2.540.27211700.27111506100
2.54-2.590.26911530.25011444100
2.59-2.650.31541630.2521498100
2.65-2.710.2681640.26011487100
2.71-2.780.27611620.25621481100
2.78-2.850.30141660.25751496100
2.85-2.940.2941590.2531491100
2.94-3.030.33091640.26241460100
3.03-3.140.32571680.24491521100
3.14-3.270.29091570.25161488100
3.27-3.410.27321590.23851480100
3.41-3.590.25611630.21371499100
3.59-3.820.25621630.19571489100
3.82-4.110.17691640.17291468100
4.11-4.530.18581600.16321484100
4.53-5.180.19991660.17031475100
5.18-6.530.19661690.19561486100
6.53-47.460.23221630.186147299
Refinement TLS params.Method: refined / Origin x: 12.3866 Å / Origin y: 11.1885 Å / Origin z: 23.7349 Å
111213212223313233
T0.1859 Å2-0.0515 Å20.0383 Å2-0.2672 Å2-0.0266 Å2--0.2589 Å2
L1.3231 °2-0.432 °2-0.5052 °2-0.9942 °20.0534 °2--1.4114 °2
S-0.0343 Å °-0.0487 Å °-0.1485 Å °0.0497 Å °-0.0587 Å °0.0749 Å °0.1913 Å °0.0548 Å °0.0899 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA180 - 620
2X-RAY DIFFRACTION1allA622 - 670

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