[English] 日本語
Yorodumi
- PDB-8y9v: ZIKV NS2B/NS3 protease -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8y9v
TitleZIKV NS2B/NS3 protease
Components
  • (Serine protease NS3) x 2
  • DAR-LYS-ORN-ARG
  • Serine protease subunit NS2B
KeywordsHYDROLASE / ZIKV / NS2B/NS3 protease
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 / ribonucleoside triphosphate phosphatase 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 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 / ribonucleoside triphosphate phosphatase 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 / protein-macromolecule adaptor activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / 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 / lipid binding / viral envelope / 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 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 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 / 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 / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, C.Y. / Xu, Q. / Wang, W.W. / Zhou, H. / Wang, Q.S.
Funding support China, 1items
OrganizationGrant numberCountry
Other government21ZR1471800 China
CitationJournal: To Be Published
Title: Crystallographic data collection using a multilayer monochromator on an undulator beamline at SSRF
Authors: Zhang, C.Y. / Xu, Q. / Liang, M. / Yu, L. / Li, M.J. / Zhu, Z.M. / Huang, L.Q. / Li, Q.H. / Yu, F. / Wang, Y.Z. / Zhou, H. / Wang, Q.S.
History
DepositionFeb 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

-
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: DAR-LYS-ORN-ARG


Theoretical massNumber of molelcules
Total (without water)45,9475
Polymers45,9475
Non-polymers00
Water2,936163
1
A: Serine protease subunit NS2B
B: Serine protease NS3


Theoretical massNumber of molelcules
Total (without water)22,2202
Polymers22,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-28 kcal/mol
Surface area9190 Å2
MethodPISA
2
C: Serine protease subunit NS2B
D: Serine protease NS3
E: DAR-LYS-ORN-ARG


Theoretical massNumber of molelcules
Total (without water)23,7273
Polymers23,7273
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-24 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.753, 59.753, 213.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 16354.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#3: Protein Serine protease NS3 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 17285.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#4: Protein/peptide DAR-LYS-ORN-ARG


Mass: 575.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: PEG 20% 2000, ammonium sulfate 0.2 M, sodium acetate trihydrate 0.1 M

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.924 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.924 Å / Relative weight: 1
ReflectionResolution: 1.9→45.77 Å / Num. obs: 31750 / % possible obs: 99.7 % / Redundancy: 24.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.527 / Rpim(I) all: 0.108 / Rrim(I) all: 0.539 / Χ2: 1.04 / Net I/σ(I): 7.3 / Num. measured all: 787827
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 94.9 % / Redundancy: 22 % / Rmerge(I) obs: 6.765 / Num. measured all: 42472 / Num. unique obs: 1929 / CC1/2: 0.057 / Rpim(I) all: 1.456 / Rrim(I) all: 6.933 / Χ2: 1.06 / Net I/σ(I) obs: 0.8

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.77 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 1992 6.31 %
Rwork0.217 --
obs0.219 31573 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 0 163 3067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082956
X-RAY DIFFRACTIONf_angle_d1.0624003
X-RAY DIFFRACTIONf_dihedral_angle_d8.084417
X-RAY DIFFRACTIONf_chiral_restr0.069445
X-RAY DIFFRACTIONf_plane_restr0.01516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.36731290.36331957X-RAY DIFFRACTION93
1.95-20.36151400.31772085X-RAY DIFFRACTION100
2-2.060.31081400.2922074X-RAY DIFFRACTION100
2.06-2.120.33731400.29432070X-RAY DIFFRACTION100
2.12-2.20.29061400.25812074X-RAY DIFFRACTION100
2.2-2.290.31031400.27512078X-RAY DIFFRACTION100
2.29-2.390.27711430.23282112X-RAY DIFFRACTION100
2.39-2.520.29391410.23882085X-RAY DIFFRACTION100
2.52-2.680.25221420.242107X-RAY DIFFRACTION100
2.68-2.880.251430.22292118X-RAY DIFFRACTION100
2.88-3.170.26731440.20292136X-RAY DIFFRACTION100
3.17-3.630.23131450.18852139X-RAY DIFFRACTION100
3.63-4.570.1891480.16052193X-RAY DIFFRACTION100
4.57-45.770.20361570.1932353X-RAY DIFFRACTION100
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)
18.9027-1.9372.3156.41981.28493.5618-0.25620.4613-0.6344-0.34210.00721.66921.0052-0.5713-0.25930.8209-0.0922-0.14060.30140.0110.49067.2135-31.6954-12.6963
22.58641.8288-0.11122.75552.13853.12860.12260.9178-0.2706-0.97230.34940.0438-0.0869-0.1539-0.12250.39450.075-0.01170.3248-0.05980.323818.9001-21.8428-28.289
34.3226-3.2256-2.03567.78696.16039.444-0.08980.88250.3232-0.73480.2409-0.06180.1970.5128-0.3420.4503-0.0128-0.05330.44190.00920.376210.0584-4.4596-28.0524
41.58350.30980.46343.3852-0.73232.7545-0.417-1.01180.38640.73280.3288-0.2084-0.5505-0.0215-0.2580.44950.1591-0.01820.4407-0.01830.29544.6322-3.045-8.5434
52.0603-1.75321.33431.6182-1.03271.85940.16730.6297-1.0806-0.3145-0.1136-0.02440.05050.17130.04880.4702-0.095-0.12970.2496-0.03470.429816.089-31.2813-16.6819
61.81580.07230.81682.3184-0.16084.11150.1281-0.1829-0.20180.08610.0403-0.01010.6341-0.034-0.12390.26570.0187-0.03740.24910.02720.208912.9563-22.4857-8.238
71.7534-1.08110.50543.4195-1.33672.3807-0.03090.20930.0874-0.2148-0.0590.0342-0.06290.15140.07750.21540.00210.00330.2031-0.00280.202915.5542-12.8563-21.6128
83.3037-1.20650.04641.44080.01972.8591-0.0233-0.0050.2813-0.1682-0.0025-0.2166-0.03810.00660.03080.195-0.031-0.02970.17650.01550.206510.0924-10.0363-19.622
91.5706-0.77680.5932.8704-0.19351.0529-0.6484-1.61710.16450.88370.1143-0.9735-0.23151.02130.35630.32360.0428-0.13970.76260.05410.357622.7801-13.373-8.7484
107.24152.51155.29693.45161.2494.00480.0843-0.3886-0.5773-0.24610.01270.17050.1808-0.2434-0.04271.54640.10820.39880.62530.02231.61931.4201-12.3853-14.5583
112.7212-0.32440.15256.75190.89915.76640.1908-0.0322-0.08530.0323-0.02870.32340.2401-0.8301-0.04030.1722-0.00270.03090.31690.06890.30894.8726-19.802419.0115
124.479-3.80371.17583.6801-0.56660.8288-0.9041-2.3129-0.78141.53821.14520.83380.5202-1.2898-0.07090.62510.11310.02840.6899-0.03590.393321.0603-13.484831.9481
132.2175-0.75850.61832.21060.68483.65980.34070.3313-0.3474-0.28080.0258-0.4320.37170.5237-0.27710.32510.0859-0.02970.35750.0030.297133.6245-23.821711.6651
142.1803-0.6285-0.12091.7885-1.71463.8689-0.02550.2676-0.2666-0.20230.06270.30490.0842-0.4863-0.02490.1840.0077-0.02960.28460.0040.23097.7541-19.915512.2643
151.7088-0.08940.62630.18230.00051.7287-0.1341-0.05650.12890.041-0.0004-0.1213-0.3994-0.05470.12140.27360.0506-0.01370.19780.03190.255120.0004-12.52212.0563
162.740.48961.00442.6517-0.34262.06720.1357-0.11910.09740.1873-0.1115-0.0188-0.23520.07910.03090.1940.0169-0.00040.20690.02180.189122.8606-18.110621.1289
175.23020.06420.18262.01891.82613.97980.3289-0.0937-0.5685-0.1437-0.25030.20910.3720.3435-0.05780.2128-0.0092-0.0080.27570.05250.251226.2342-20.720715.8195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 7 through 11 )
2X-RAY DIFFRACTION2chain 'C' and (resid 12 through 21 )
3X-RAY DIFFRACTION3chain 'C' and (resid 22 through 31 )
4X-RAY DIFFRACTION4chain 'C' and (resid 32 through 44 )
5X-RAY DIFFRACTION5chain 'D' and (resid 13 through 34 )
6X-RAY DIFFRACTION6chain 'D' and (resid 35 through 79 )
7X-RAY DIFFRACTION7chain 'D' and (resid 80 through 118 )
8X-RAY DIFFRACTION8chain 'D' and (resid 119 through 163 )
9X-RAY DIFFRACTION9chain 'D' and (resid 164 through 173 )
10X-RAY DIFFRACTION10chain 'E' and (resid 2 through 4 )
11X-RAY DIFFRACTION11chain 'A' and (resid 7 through 16 )
12X-RAY DIFFRACTION12chain 'A' and (resid 17 through 26 )
13X-RAY DIFFRACTION13chain 'A' and (resid 27 through 45 )
14X-RAY DIFFRACTION14chain 'B' and (resid 18 through 71 )
15X-RAY DIFFRACTION15chain 'B' and (resid 72 through 94 )
16X-RAY DIFFRACTION16chain 'B' and (resid 95 through 155 )
17X-RAY DIFFRACTION17chain 'B' and (resid 156 through 170 )

+
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