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- PDB-5h6v: Structure of Zika virus protease in complex with a dipeptide inhibitor -

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Basic information

Entry
Database: PDB / ID: 5h6v
TitleStructure of Zika virus protease in complex with a dipeptide inhibitor
Components(Genome polyprotein) x 2
KeywordsVIRAL PROTEIN/INHIBITOR / SERINE PROTEASE / NON-STRUCTURAL PROTEIN 3 / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell ...ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 ...Thrombin, subunit H - #120 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 / Trypsin-like serine proteases / Thrombin, subunit H / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-7HS / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.422 Å
AuthorsZhang, Z. / Chen, M.
Funding support Singapore, 2items
OrganizationGrant numberCountry
NTUSTART UP GRANT Singapore
NMRCCBRG14May05 Singapore
CitationJournal: Structure / Year: 2017
Title: Structural Dynamics of Zika Virus NS2B-NS3 Protease Binding to Dipeptide Inhibitors
Authors: Li, Y. / Zhang, Z. / Phoo, W.W. / Loh, Y.R. / Wang, W. / Liu, S. / Chen, M.W. / Hung, A.W. / Keller, T.H. / Luo, D. / Kang, C.
History
DepositionNov 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0883
Polymers24,7602
Non-polymers3281
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-27 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.330, 42.330, 214.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-307-

HOH

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Components

#1: Protein Genome polyprotein


Mass: 5750.296 Da / Num. of mol.: 1 / Fragment: UNP residues 1411-1462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: H8XX12
#2: Protein Genome polyprotein


Mass: 19009.578 Da / Num. of mol.: 1 / Fragment: UNP residues 1497-1673 / Mutation: R29K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: H8XX12
#3: Chemical ChemComp-7HS / (S)-2-acetamido-6-amino-N-((S)-5-guanidino-1-oxopentan-2-yl)hexanamide


Mass: 328.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28N6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 2M Ammonium sulfate, 0.1M Sodium acetate trihydrate PH4.6
PH range: 4.0-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0004 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 2.42→42.95 Å / Num. obs: 8233 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Net I/σ(I): 21.5
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 833 / Rpim(I) all: 0.337 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SHELXL(1.10.1_2155: ???)data collection
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPI

5gpi


Resolution: 2.422→42.33 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 440 5.41 %
Rwork0.1912 --
obs0.1944 8137 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.422→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 23 21 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081481
X-RAY DIFFRACTIONf_angle_d0.9482011
X-RAY DIFFRACTIONf_dihedral_angle_d19.466870
X-RAY DIFFRACTIONf_chiral_restr0.055225
X-RAY DIFFRACTIONf_plane_restr0.007262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4216-2.7720.34691320.25442484X-RAY DIFFRACTION100
2.772-3.49220.27321500.20882523X-RAY DIFFRACTION100
3.4922-42.33590.21331580.17012690X-RAY DIFFRACTION99
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)
10.00310.01070.00070.01110.00380.00360.14260.11920.1723-0.01180.07980.0572-0.1127-0.043400.7350.25750.14020.53760.0410.4347-24.292914.6791-12.9562
20.00470.0104-0.00660.0519-0.00070.0049-0.0892-0.03510.128-0.0087-0.02740.1225-0.0275-0.01400.56140.1249-0.1440.33680.02250.7048-28.17514.2934-23.8076
30.1660.0986-0.00140.0709-0.02450.0704-0.14660.04230.0402-0.252-0.0169-0.0587-0.19240.1033-0.07430.97190.473-0.10370.6935-0.01640.0662-18.5739-4.2974-32.8481
40.08650.0053-0.02840.0497-0.01680.0153-0.03350.02760.02790.00830.03170.0913-0.0026-0.0144-0.00090.30660.23050.00010.5789-0.11030.9336-3.5617-11.1837-22.7287
50.0090.0091-0.01580.0317-0.02090.02850.1732-0.02310.14220.00420.1253-0.28540.0341-0.060.00860.26540.1383-0.01240.58910.04010.4754-3.6123-5.4546-7.5229
60.0573-0.01370.08460.011-0.04680.10810.00860.04780.2794-0.3136-0.0494-0.34970.052-0.0944-0.00370.51160.1580.02270.3613-0.02530.4175-23.290610.8971-16.4732
70.07180.10420.02540.2190.01640.03360.547-0.27850.10340.3722-0.22330.2019-0.2118-0.12110.13590.3820.16990.12960.21610.0150.4125-22.91214.3092-7.0225
80.53210.36770.01490.48920.17970.13730.3643-0.0581-0.0091-0.0273-0.3321-0.04620.24910.21050.02320.44750.2019-0.06760.3073-0.00880.284-21.9499-9.6984-16.4364
90.26630.2038-0.08510.390.15060.12880.46190.3188-0.0796-0.4551-0.4136-0.0024-0.05290.18110.19660.50840.32710.08310.53480.02390.3359-13.753-3.3396-20.1417
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 42 )
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 79 )
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 94 )
9X-RAY DIFFRACTION9chain 'B' and (resid 95 through 171 )

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