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- PDB-7h1r: PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2... -

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Basic information

Entry
Database: PDB / ID: 7h1r
TitlePanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with Z270758780
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


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
: / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.521 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

Downloads & links

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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)23,4935
Polymers23,1852
Non-polymers3073
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-24 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.797, 42.797, 216.836
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-A1AJP / 4-(aminomethyl)-N,N-dimethylpyridin-2-amine


Mass: 151.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.14 Å3/Da / Density % sol: 42.56 %
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 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.52→39.8 Å / Num. obs: 32457 / % possible obs: 100 % / Redundancy: 25 % / CC1/2: 0.988 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.034 / Rrim(I) all: 0.168 / Χ2: 0.59 / Net I/σ(I): 9.2 / Num. measured all: 811032
Reflection shellResolution: 1.52→1.55 Å / % possible obs: 99.6 % / Redundancy: 20.2 % / Num. measured all: 31244 / Num. unique obs: 1543 / CC1/2: 0.386 / Rpim(I) all: 2.931 / Rrim(I) all: 13.413 / Χ2: 0.36 / Net I/σ(I) obs: 0.2

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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: 1.521→19.34 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1604 5.1 %RANDOM
Rwork0.2227 ---
obs0.224 31443 97.3 %-
Displacement parametersBiso mean: 48.09 Å2
Baniso -1Baniso -2Baniso -3
1--5.385 Å20 Å20 Å2
2---5.385 Å20 Å2
3---10.7701 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.521→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 19 141 1636
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011651HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12264HARMONIC2
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_planes295HARMONIC5
X-RAY DIFFRACTIONt_it1651HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.92
X-RAY DIFFRACTIONt_other_torsion15.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion208SEMIHARMONIC5
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_contact1381SEMIHARMONIC4
LS refinement shellResolution: 1.52→1.54 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.5009 40 6.36 %
Rwork0.5634 589 -
all0.5595 629 -
obs--45.89 %
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)
12.8658-1.98760.9923.54310.4763.40790.40820.45070.2356-0.5756-0.4007-0.2109-0.1120.6139-0.00750.00340.12250.1006-0.00720.0685-0.1691-14.8005-1.2004-19.9251
21.1108-0.98140.9191.08010.04542.43930.24420.13280.0682-0.2074-0.26770.0697-0.04910.25510.02350.07150.09820.0225-0.01440.018-0.0241-18.87631.4791-15.5624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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