[English] 日本語
Yorodumi
- PDB-7vxy: Zika virus NS2B/NS3 protease bZipro(C143S) in complex with D-RKOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vxy
TitleZika virus NS2B/NS3 protease bZipro(C143S) in complex with D-RKOR
Components
  • Peptide inhibitor
  • Serine protease NS3
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / ZIKV / NS2B/NS3 protease / inhibitor / complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / symbiont entry into host cell / GTP binding / 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
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
Biological speciesZika virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.901 Å
AuthorsXiong, Y.C. / Cheng, F. / Zhang, J.Y. / Su, H.X. / Hu, H.C. / Zou, Y. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Chem. / Year: 2022
Title: Structure-based design of a novel inhibitor of the ZIKA virus NS2B/NS3 protease.
Authors: Xiong, Y. / Cheng, F. / Zhang, J. / Su, H. / Hu, H. / Zou, Y. / Li, M. / Xu, Y.
History
DepositionNov 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine protease subunit NS2B
B: Serine protease NS3
C: Serine protease subunit NS2B
D: Serine protease NS3
E: Peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)52,1565
Polymers52,1565
Non-polymers00
Water2,702150
1
A: Serine protease subunit NS2B
B: Serine protease NS3


Theoretical massNumber of molelcules
Total (without water)25,7902
Polymers25,7902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-27 kcal/mol
Surface area9170 Å2
MethodPISA
2
C: Serine protease subunit NS2B
D: Serine protease NS3
E: Peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)26,3663
Polymers26,3663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-26 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.574, 59.574, 213.809
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Serine protease subunit NS2B


Mass: 5865.384 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H8XX12
#2: Protein Serine protease NS3


Mass: 19924.557 Da / Num. of mol.: 2 / Mutation: C143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: H8XX12, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#3: Protein/peptide Peptide inhibitor


Mass: 575.728 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 33.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulfate, 30% polyethylene glycol monomethyl ether 2000, 0.1M sodium acetate trihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 31082 / % possible obs: 98.5 % / Redundancy: 20.9 % / Biso Wilson estimate: 18.67 Å2 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.035 / Rrim(I) all: 0.167 / Χ2: 1.046 / Net I/σ(I): 4.3 / Num. measured all: 650874
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9319.70.66914730.9440.1440.6860.52495
1.93-1.9720.40.59314670.950.1260.6080.57297
1.97-2.0120.70.55214940.9630.1170.5650.61595.5
2.01-2.0520.50.52315100.9640.1110.5350.65798.3
2.05-2.0920.30.49314820.9510.1060.5050.70497.9
2.09-2.1420.40.43715060.9690.0930.4480.7797.2
2.14-2.1922.10.37415340.9780.0770.3820.82898.3
2.19-2.2522.40.33115010.9880.0680.3380.90498.2
2.25-2.3221.90.32715320.980.0680.3350.95798.5
2.32-2.3921.50.30715390.9860.0650.3141.04998.5
2.39-2.4820.90.31115490.9690.0670.3191.198.5
2.48-2.5820.10.28515420.9820.0620.2921.20699.5
2.58-2.721.20.24915580.9880.0530.2551.35399.4
2.7-2.8421.80.22215650.9890.0470.2271.48899.3
2.84-3.0221.60.20715640.9870.0440.2121.5899.5
3.02-3.2520.40.18215800.9930.040.1871.61599.8
3.25-3.5820.30.15516010.9950.0340.1591.523100
3.58-4.0921.30.12816120.9970.0280.1321.293100
4.09-5.1619.70.10916630.9990.0240.1121.061100
5.16-5021.40.10718100.9980.0230.1090.938100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.45 Å45.71 Å
Translation5.45 Å45.71 Å

-
Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LC0

5lc0


Resolution: 1.901→45.708 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 1453 4.88 %
Rwork0.2033 28314 -
obs0.2057 29767 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.99 Å2 / Biso mean: 25.9921 Å2 / Biso min: 8.66 Å2
Refinement stepCycle: final / Resolution: 1.901→45.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 40 150 3054
Biso mean--37.97 32.7 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052956
X-RAY DIFFRACTIONf_angle_d0.7624003
X-RAY DIFFRACTIONf_chiral_restr0.054445
X-RAY DIFFRACTIONf_plane_restr0.005516
X-RAY DIFFRACTIONf_dihedral_angle_d7.2711726
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.901-1.96890.30341020.2322209772
1.9689-2.04770.26351380.2141258788
2.0477-2.14090.2911240.2119275094
2.1409-2.25380.25441510.1986283397
2.2538-2.3950.23561530.2097289098
2.395-2.57990.30091450.228293699
2.5799-2.83950.28841640.2189294999
2.8395-3.25030.26811600.20582973100
3.2503-4.09460.23851570.18623040100
4.0946-45.7080.2041590.19163259100
Refinement TLS params.Method: refined / Origin x: 43.9525 Å / Origin y: 17.1166 Å / Origin z: 106.4927 Å
111213212223313233
T0.0889 Å20.0074 Å20.0212 Å2-0.0976 Å2-0.0143 Å2--0.1481 Å2
L0.3648 °2-0.1554 °2-0.5389 °2-0.5151 °20.4695 °2--2.2197 °2
S-0.013 Å °0.0301 Å °0.0348 Å °-0.0376 Å °-0.0079 Å °-0.0623 Å °0.0058 Å °-0.0249 Å °0.0232 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 45
2X-RAY DIFFRACTION1allB18 - 170
3X-RAY DIFFRACTION1allC7 - 44
4X-RAY DIFFRACTION1allD13 - 201
5X-RAY DIFFRACTION1allS1 - 150

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more