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- PDB-7ga2: PanDDA analysis group deposition -- Crystal Structure of Zika vir... -

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Basic information

Entry
Database: PDB / ID: 7ga2
TitlePanDDA analysis group deposition -- Crystal Structure of Zika virus NS3 Helicase in complex with POB0008
ComponentsSerine protease NS3
KeywordsVIRAL PROTEIN / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / 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 / induction by virus of host autophagy / 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 / lipid binding / viral envelope / host cell nucleus / GTP binding / 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 capsid protein C superfamily / 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 superfamily / 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
PHOSPHATE ION / methyl 1-(methanesulfonyl)-2-methyl-D-prolinate / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.034 Å
AuthorsGodoy, A.S. / Noske, G.D. / Fairhead, M. / Lithgo, R.M. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Ni, X. / Tomlinson, C.W.E. ...Godoy, A.S. / Noske, G.D. / Fairhead, M. / Lithgo, R.M. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Ni, X. / Tomlinson, C.W.E. / Wild, C. / Mesquita, N.C.M.R. / Oliva, G. / Fearon, D. / Walsh, M.A. / von Delft, F.
Funding support United States, Brazil, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171399 United States
Sao Paulo Research Foundation (FAPESP)2013/07600-3 Brazil
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Godoy, A.S. / Noske, G.D. / Fairhead, M. / Lithgo, R.M. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Ni, X. / Tomlinson, C.W.E. / Wild, C. / Mesquita, N.C.M.R. / ...Authors: Godoy, A.S. / Noske, G.D. / Fairhead, M. / Lithgo, R.M. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Ni, X. / Tomlinson, C.W.E. / Wild, C. / Mesquita, N.C.M.R. / Oliva, G. / Fearon, D. / Walsh, M.A. / von Delft, F.
History
DepositionJul 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)49,4235
Polymers48,9501
Non-polymers4734
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.985, 70.044, 57.789
Angle α, β, γ (deg.)90.000, 92.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine protease NS3 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 48950.008 Da / Num. of mol.: 1 / Fragment: HELICASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-YEK / methyl 1-(methanesulfonyl)-2-methyl-D-prolinate


Mass: 221.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.23 Å3/Da / Density % sol: 44.85 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M NPS Mix (0.3 M Sodium phosphate dibasic dihydrate, 0.3 M Ammonium sulphate and 0.3 M Sodium nitrate - Molecular Dimensions), 0.1 M MES/Imidazole pH 6.5 (Molecular Dimensions) and 33% ...Details: 0.12 M NPS Mix (0.3 M Sodium phosphate dibasic dihydrate, 0.3 M Ammonium sulphate and 0.3 M Sodium nitrate - Molecular Dimensions), 0.1 M MES/Imidazole pH 6.5 (Molecular Dimensions) and 33% Precipitant Mix 4 (11% MPD, 11% PEG 1,000 e 11% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 2.04→70.02 Å / Num. obs: 27458 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 33.42 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.093 / Rrim(I) all: 0.243 / Net I/σ(I): 5.2 / Num. measured all: 189622 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.04-2.17.11.6991350619120.1850.6981.840.789.2
8.9-70.0260.07821493580.9820.0360.08629.599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.4 (17-FEB-2023)refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5RHY

5rhy


Resolution: 2.034→19.34 Å / Cor.coef. Fo:Fc: 0.823 / Cor.coef. Fo:Fc free: 0.8 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.261 / SU Rfree Blow DPI: 0.215 / SU Rfree Cruickshank DPI: 0.211
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 1264 4.62 %RANDOM
Rwork0.2111 ---
obs0.2141 27333 98.5 %-
Displacement parametersBiso max: 280.23 Å2 / Biso mean: 39.97 Å2 / Biso min: 25.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.9564 Å20 Å210.5724 Å2
2--26.052 Å20 Å2
3----28.0084 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.034→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 28 352 3813
Biso mean--74.67 47.38 -
Num. residues----435
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1271SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes606HARMONIC5
X-RAY DIFFRACTIONt_it3560HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion470SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2891SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3560HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4829HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion16.65
LS refinement shellResolution: 2.03→2.06 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3819 33 6.03 %
Rwork0.3968 514 -
all-547 -
obs--58.79 %
Refinement TLS params.Method: refined / Origin x: -13.75 Å / Origin y: 1.2345 Å / Origin z: -20.743 Å
111213212223313233
T-0.0083 Å2-0.0053 Å20.1309 Å2-0.2995 Å2-0.0207 Å2---0.3056 Å2
L0.2264 °20.0335 °2-0.0194 °2-0.5016 °2-0.1455 °2--0.2079 °2
S0.0338 Å °-0.0155 Å °0.0306 Å °0.0207 Å °-0.0371 Å °0.0154 Å °0.0087 Å °0.026 Å °0.0032 Å °
Refinement TLS groupSelection details: { A|* }

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