[English] 日本語
Yorodumi
- PDB-1vzv: STRUCTURE OF VARICELLA-ZOSTER VIRUS PROTEASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vzv
TitleSTRUCTURE OF VARICELLA-ZOSTER VIRUS PROTEASE
ComponentsVARICELLA-ZOSTER VIRUS PROTEASE
KeywordsSERINE PROTEASE / HYDROLASE / VIRAL PROTEASE / VARICELLA-ZOSTER VIRUS / COAT PROTEIN
Function / homology
Function and homology information


nuclear capsid assembly / assemblin / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / identical protein binding
Similarity search - Function
Serine Protease, Human Cytomegalovirus Protease; Chain A / Herpesvirus/Caudovirus protease domain / Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21) / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 3 (Varicella-zoster virus)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsQiu, X. / Jason, C.A. / Culp, J.S. / Richardson, S.B. / Debouck, C. / Smith, W.W. / Abdel-Meguid, S.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Crystal structure of varicella-zoster virus protease.
Authors: Qiu, X. / Janson, C.A. / Culp, J.S. / Richardson, S.B. / Debouck, C. / Smith, W.W. / Abdel-Meguid, S.S.
#1: Journal: Nature / Year: 1996
Title: Unique Fold and Active Site in Cytomegalovirus Protease
Authors: Qiu, X. / Culp, J.S. / Dilella, A.G. / Hellmig, B. / Hoog, S.S. / Janson, C.A. / Smith, W.W. / Abdel-Meguid, S.S.
History
DepositionFeb 10, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VARICELLA-ZOSTER VIRUS PROTEASE


Theoretical massNumber of molelcules
Total (without water)24,6551
Polymers24,6551
Non-polymers00
Water0
1
A: VARICELLA-ZOSTER VIRUS PROTEASE

A: VARICELLA-ZOSTER VIRUS PROTEASE


Theoretical massNumber of molelcules
Total (without water)49,3092
Polymers49,3092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+2/31
Buried area2600 Å2
ΔGint-17 kcal/mol
Surface area19080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.000, 90.000, 117.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein VARICELLA-ZOSTER VIRUS PROTEASE / ASSEMBLIN


Mass: 24654.525 Da / Num. of mol.: 1 / Fragment: RESIDUES 10 - 236 / Mutation: C10M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 3 (Varicella-zoster virus)
Genus: Varicellovirus / Strain: ACYCLOVIR-RESISTANT STRAIN 40A2 / Production host: Escherichia coli (E. coli)
References: UniProt: P09286, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 60 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Mphosphate1reservoir
22.5 M1reservoirNaCl
310 mg/mlprotein1drop

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 28, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 5419 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Highest resolution: 3 Å

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing
RefinementResolution: 3→7 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.223 -
obs0.223 4903
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 0 0 1623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_deg1.8

+
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