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- PDB-8um3: PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase i... -

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Entry
Database: PDB / ID: 8um3
TitlePanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z203039992
ComponentsZika virus NS3 helicase domain
KeywordsHYDROLASE / zika virus helicase / VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host interferon-mediated signaling pathway / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / protein-macromolecule adaptor activity ...symbiont-mediated suppression of host interferon-mediated signaling pathway / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / protein-macromolecule adaptor activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis 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 / 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 / 6-chlorotetrazolo[1,5-b]pyridazine / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.925 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) Brazil
CitationJournal: To Be Published
Title: PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z203039992
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
DepositionOct 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.grant_number
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zika virus NS3 helicase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4766
Polymers48,9501
Non-polymers5265
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.644, 69.588, 57.552
Angle α, β, γ (deg.)90.00, 92.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Zika virus NS3 helicase domain


Mass: 48950.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q32ZE1, RNA helicase

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Non-polymers , 5 types, 378 molecules

#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-W41 / 6-chlorotetrazolo[1,5-b]pyridazine


Mass: 155.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H2ClN5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.925→57.51 Å / Num. obs: 32130 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.076 / Rrim(I) all: 0.199 / Χ2: 0.98 / Net I/σ(I): 7.4
Reflection shellResolution: 1.93→2.03 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.902 / Num. measured all: 32621 / Num. unique obs: 4613 / CC1/2: 0.42 / Rpim(I) all: 0.764 / Rrim(I) all: 2.051 / Χ2: 0.95 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (17-FEB-2023)refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.925→25.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.187 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.159
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1474 4.6 %RANDOM
Rwork0.1906 ---
obs0.1928 32071 99.8 %-
Displacement parametersBiso mean: 34.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.6676 Å20 Å20.7408 Å2
2--0.2318 Å20 Å2
3----1.8994 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.925→25.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 31 373 3837
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083555HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.914817HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1258SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes615HARMONIC5
X-RAY DIFFRACTIONt_it3555HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion15.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion468SEMIHARMONIC5
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_contact3157SEMIHARMONIC4
LS refinement shellResolution: 1.93→1.94 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3022 -4.67 %
Rwork0.2967 612 -
all0.2969 642 -
obs--94.81 %
Refinement TLS params.Method: refined / Origin x: -13.7511 Å / Origin y: 1.176 Å / Origin z: -20.6239 Å
111213212223313233
T-0.0223 Å2-0.0077 Å20.0157 Å2--0.0419 Å2-0.0099 Å2--0.0208 Å2
L0.1691 °2-0.0281 °2-0.0175 °2-0.3833 °2-0.1349 °2--0.1101 °2
S0.0353 Å °-0.0079 Å °0.0474 Å °0.0192 Å °-0.0193 Å °0.0048 Å °0.0246 Å °0.0259 Å °-0.0161 Å °
Refinement TLS groupSelection details: { A|* }

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