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- PDB-29hn: Crystal structure of Zika virus NS2B-NS3 protease determined via ... -

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Basic information

Entry
Database: PDB / ID: 29hn
TitleCrystal structure of Zika virus NS2B-NS3 protease determined via sulfur phasing
Components
  • Serine protease NS3
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / Zika Virus / NS2B-NS3 protease / Diamond Light Source / Beamline i23 / sulfur phasing / long wavelength / OpenBind Consortium
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 / clathrin-dependent endocytosis of virus by host cell ...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 / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell cytoplasm / protein-macromolecule adaptor activity / methyltransferase cap1 activity / 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 / serine-type endopeptidase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / virion attachment to host cell / GTP binding / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / 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 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 superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation 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
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.774 Å
AuthorsMarples, P.G. / Duman, R. / Ebrahim, A. / Chinn, C.A. / Cooper, M.R. / Keates, T. / V.Chandran, A. / Ni, X. / Wang, S. / Williams, E. ...Marples, P.G. / Duman, R. / Ebrahim, A. / Chinn, C.A. / Cooper, M.R. / Keates, T. / V.Chandran, A. / Ni, X. / Wang, S. / Williams, E. / Koekemoer, L. / Fairhead, M. / Wagner, A. / Shotton, E.J. / Aschenbrenner, J.C. / von Delft, F. / Open Bind Consortium
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other governmentG2-SCH-2025-06-16537 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of Zika virus NS2B-NS3 protease determined via sulfur phasing
Authors: Marples, P.G. / Duman, R. / Ebrahim, A. / Chinn, C.A. / Cooper, M.R. / Keates, T. / V.Chandran, A. / Ni, X. / Wang, S. / Williams, E. / Koekemoer, L. / Fairhead, M. / Wagner, A. / Shotton, E. ...Authors: Marples, P.G. / Duman, R. / Ebrahim, A. / Chinn, C.A. / Cooper, M.R. / Keates, T. / V.Chandran, A. / Ni, X. / Wang, S. / Williams, E. / Koekemoer, L. / Fairhead, M. / Wagner, A. / Shotton, E.J. / Aschenbrenner, J.C. / von Delft, F.
History
DepositionMar 12, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)23,1852
Polymers23,1852
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-23 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.541, 42.541, 215.365
Angle α, β, γ (deg.)90, 90, 90
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
Details: Zika virus NS2B co-factor region co-expressed with Zika virus NS3 protease
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21 (bacteria) / 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.1 M sodium acetate, pH 4.8, 0.2 M ammonium sulfate, 30 % w/v PEG2000

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Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jan 28, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 1.774→53.841 Å / Num. obs: 16590 / % possible obs: 91.8 % / Redundancy: 42.5 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.009 / Rrim(I) all: 0.069 / Net I/σ(I): 29
Reflection shellResolution: 1.774→1.855 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.159 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 829 / CC1/2: 0.885 / Rpim(I) all: 0.316 / Rrim(I) all: 1.207 / % possible all: 79.5

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
GDAdata collection
Aimless0.8.2data scaling
CRANK2phasing
autoPROCdata processing
STARANISOdata scaling
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.774→53.84 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.164 / SU Rfree Cruickshank DPI: 0.157
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 823 -RANDOM
Rwork0.2195 15766 --
obs0.2217 16589 81.8 %-
Displacement parametersBiso mean: 32.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.5835 Å20 Å20 Å2
2--1.5835 Å20 Å2
3----3.1671 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 1.774→53.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 0 119 1593
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091538HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.012092HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d526SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes267HARMONIC5
X-RAY DIFFRACTIONt_it1538HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion192SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1314SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.76
X-RAY DIFFRACTIONt_other_torsion14.6
LS refinement shellResolution: 1.774→1.82 Å
RfactorNum. reflection% reflection
Rfree0.3862 17 -
Rwork0.2782 388 -
obs--29.96 %
Refinement TLS params.

T12: -0.152 Å2 / 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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5031.4426-0.26412.84461.10112.67110.3215-0.2243-0.15180.4661-0.2227-0.26460.23870.2932-0.09880.0259-0.1099-0.03980.0955-0.13917.174822.773619.3543
20.88090.7462-0.69740.6791-0.11171.19490.2815-0.1217-0.09010.1092-0.26270.062-0.06180.1572-0.01880.1057-0.0330.04780.0351-0.07212.712520.706415.6605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A50 - 87
2X-RAY DIFFRACTION2{ B|* }B17 - 172

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