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- PDB-7h1i: PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2... -

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Basic information

Entry
Database: PDB / ID: 7h1i
TitlePanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with Z336080990
Components
  • Serine protease NS3
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / ASAP / AViDD / 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 / 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 / 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 / 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 / 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 / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / : / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell nucleus / virion attachment to host cell / GTP binding / 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 / : / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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. / 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 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 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 / : / Flavivirus NS3 helicase, C-terminal helical domain / 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
N-(propan-2-yl)-1H-benzimidazol-2-amine / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.414 Å
AuthorsNi, X. / Godoy, A.S. / Marples, P.G. / Fairhead, M. / Balcomb, B.H. / Tomlinson, C.W.E. / Koekemoer, L. / Aschenbrenner, J.C. / Lithgo, R.M. / Thompson, W. ...Ni, X. / Godoy, A.S. / Marples, P.G. / Fairhead, M. / Balcomb, B.H. / Tomlinson, C.W.E. / Koekemoer, L. / Aschenbrenner, J.C. / Lithgo, R.M. / Thompson, W. / Wild, C. / Williams, E.P. / Winokan, M. / Chandran, A.V. / Fearon, D. / Walsh, M.A. / von Delft, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171399 United States
CitationJournal: To Be Published
Title: PanDDA analysis group deposition of ZIKV NS2B-NS3 protease
Authors: Ni, X. / Godoy, A.S. / Marples, P.G. / Fairhead, M. / Balcomb, B.H. / Tomlinson, C.W.E. / Koekemoer, L. / Aschenbrenner, J.C. / Lithgo, R.M. / Thompson, W. / Wild, C. / Williams, E.P. / ...Authors: Ni, X. / Godoy, A.S. / Marples, P.G. / Fairhead, M. / Balcomb, B.H. / Tomlinson, C.W.E. / Koekemoer, L. / Aschenbrenner, J.C. / Lithgo, R.M. / Thompson, W. / Wild, C. / Williams, E.P. / Winokan, M. / Chandran, A.V. / Fearon, D. / Walsh, M.A. / von Delft, F.
History
DepositionApr 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease subunit NS2B
B: Serine protease NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5175
Polymers23,1852
Non-polymers3313
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-24 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.574, 42.574, 216.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein/peptide Serine protease subunit NS2B / Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B


Mass: 5067.486 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
#2: Protein Serine protease NS3 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 18117.629 Da / Num. of mol.: 1 / Mutation: None
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
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-VWJ / N-(propan-2-yl)-1H-benzimidazol-2-amine


Mass: 175.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 30% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.41→72.17 Å / Num. obs: 39982 / % possible obs: 100 % / Redundancy: 23.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.014 / Rrim(I) all: 0.069 / Χ2: 0.31 / Net I/σ(I): 13.7 / Num. measured all: 943402
Reflection shellResolution: 1.41→1.43 Å / % possible obs: 99.9 % / Redundancy: 16.5 % / Rmerge(I) obs: 9.615 / Num. measured all: 32071 / Num. unique obs: 1941 / CC1/2: 0.457 / Rpim(I) all: 2.416 / Rrim(I) all: 9.92 / Χ2: 0.08 / Net I/σ(I) obs: 0.1

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.414→25.02 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.088 / SU Rfree Blow DPI: 0.086 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1737 5.05 %RANDOM
Rwork0.2213 ---
obs0.2226 34380 86.9 %-
Displacement parametersBiso mean: 50.87 Å2
Baniso -1Baniso -2Baniso -3
1--6.1451 Å20 Å20 Å2
2---6.1451 Å20 Å2
3---12.2903 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 1.414→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 21 138 1635
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111652HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.072265HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d558SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes300HARMONIC5
X-RAY DIFFRACTIONt_it1652HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.06
X-RAY DIFFRACTIONt_other_torsion15.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion206SEMIHARMONIC5
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_contact1418SEMIHARMONIC4
LS refinement shellResolution: 1.41→1.49 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.585 39 5.67 %
Rwork0.6141 649 -
all0.6126 688 -
obs--12.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2181-1.79061.10063.58530.87442.8480.57590.57550.3757-0.5739-0.5126-0.3068-0.10340.5909-0.06320.04950.23580.14830.06760.1296-0.1635-14.4306-1.6619-19.8507
21.3716-0.93380.95480.9150.02551.64230.37490.21170.1856-0.1826-0.38030.03860.07160.25680.00540.1120.19810.06480.06260.0575-0.0104-18.16740.8891-15.6106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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