[English] 日本語
Yorodumi
- PDB-9eqo: N-terminal domain Infectious Bursal Disease Virus (IBDV) VP3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9eqo
TitleN-terminal domain Infectious Bursal Disease Virus (IBDV) VP3
ComponentsCapsid protein VP3
KeywordsVIRAL PROTEIN / dsRNA binding protein / Birnavirus / IBDV / VP3
Function / homology
Function and homology information


T=13 icosahedral viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / host cell cytoplasm / structural molecule activity / proteolysis / identical protein binding / metal ion binding
Similarity search - Function
Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Viral coat protein subunit
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesInfectious bursal disease virus (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.34 Å
AuthorsFerrero, D.S. / Verdaguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117976GB-I00 Spain
CitationJournal: To Be Published
Title: Structure of the amino terminal domain of the Birnaviral multifunctional VP3 protein and its unexplored critical role
Authors: Ferrero, D.S. / Verdaguer, N.
History
DepositionMar 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein VP3
B: Capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)14,4442
Polymers14,4442
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-45 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.952, 54.952, 89.468
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Capsid protein VP3


Mass: 7222.065 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bursal disease virus (Gumboro virus)
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61825
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.5M NaCl, 0.1M Sodium Acetate pH4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0396 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0396 Å / Relative weight: 1
ReflectionResolution: 1.34→47.59 Å / Num. obs: 35270 / % possible obs: 98.56 % / Redundancy: 17.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0559 / Rpim(I) all: 0.0133 / Rrim(I) all: 0.0575 / Net I/σ(I): 22.1
Reflection shellResolution: 1.34→1.38 Å / Rmerge(I) obs: 0.9654 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 20955 / CC1/2: 0.815 / Rpim(I) all: 0.3288 / Rrim(I) all: 0.918

-
Processing

Software
NameVersionClassification
PHENIX(dev_4788: ???)refinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.34→47.59 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1729 1772 5.02 %Random selection
Rwork0.1617 ---
obs0.1623 35270 98.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.34→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 0 145 1120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.98
X-RAY DIFFRACTIONf_dihedral_angle_d12.253356
X-RAY DIFFRACTIONf_chiral_restr0.069150
X-RAY DIFFRACTIONf_plane_restr0.009182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.380.29051500.25922210X-RAY DIFFRACTION87
1.38-1.420.23731390.21932448X-RAY DIFFRACTION96
1.42-1.460.1831090.16132548X-RAY DIFFRACTION99
1.46-1.510.17931540.1362562X-RAY DIFFRACTION100
1.51-1.580.18391260.1322602X-RAY DIFFRACTION100
1.58-1.650.19551370.14772588X-RAY DIFFRACTION100
1.65-1.730.20611060.17712617X-RAY DIFFRACTION100
1.73-1.840.17781500.15942610X-RAY DIFFRACTION100
1.84-1.980.15621290.14212610X-RAY DIFFRACTION100
1.99-2.180.17351210.14952635X-RAY DIFFRACTION100
2.19-2.50.14231460.14252636X-RAY DIFFRACTION100
2.5-3.150.16091350.16452659X-RAY DIFFRACTION100
3.15-47.590.17751700.17292773X-RAY DIFFRACTION100

+
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