[English] 日本語
Yorodumi
- PDB-2df7: Crystal structure of infectious bursal disease virus VP2 subviral... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2df7
TitleCrystal structure of infectious bursal disease virus VP2 subviral particle
Componentsstructural polyprotein VP2
KeywordsVIRUS LIKE PARTICLE / icosahedral capsid / immunogen / epitope / surface loop
Function / homology
Function and homology information


host cell surface binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / Hsp90 protein binding / viral capsid / host cell surface / host cell cytoplasm / host cell plasma membrane / structural molecule activity / metal ion binding / cytoplasm
Similarity search - Function
icosahedral virus / 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. ...icosahedral virus / 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. / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesInfectious bursal disease virus (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKo, T.P. / Lee, C.C. / Wang, M.Y. / Wang, A.H.
Citation
Journal: J.Struct.Biol. / Year: 2006
Title: Crystal structure of infectious bursal disease virus VP2 subviral particle at 2.6A resolution: Implications in virion assembly and immunogenicity.
Authors: Lee, C.C. / Ko, T.P. / Chou, C.C. / Yoshimura, M. / Doong, S.R. / Wang, M.Y. / Wang, A.H.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Purification, crystallization and preliminary X-ray analysis of immunogenic virus-like particles formed by infectious bursal disease virus (IBDV) structural protein VP2
Authors: Lee, C.C. / Ko, T.P. / Lee, M.S. / Chou, C.C. / Lai, S.Y. / Wang, A.H.J. / Wang, M.Y.
History
DepositionFeb 27, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 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: structural polyprotein VP2
B: structural polyprotein VP2
C: structural polyprotein VP2
D: structural polyprotein VP2
E: structural polyprotein VP2
F: structural polyprotein VP2
G: structural polyprotein VP2
H: structural polyprotein VP2
I: structural polyprotein VP2
J: structural polyprotein VP2
K: structural polyprotein VP2
L: structural polyprotein VP2
M: structural polyprotein VP2
N: structural polyprotein VP2
O: structural polyprotein VP2
P: structural polyprotein VP2
Q: structural polyprotein VP2
R: structural polyprotein VP2
S: structural polyprotein VP2
T: structural polyprotein VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)987,25336
Polymers986,64920
Non-polymers60416
Water80,0774445
1
A: structural polyprotein VP2
B: structural polyprotein VP2
C: structural polyprotein VP2
D: structural polyprotein VP2
E: structural polyprotein VP2
F: structural polyprotein VP2
G: structural polyprotein VP2
H: structural polyprotein VP2
I: structural polyprotein VP2
J: structural polyprotein VP2
K: structural polyprotein VP2
L: structural polyprotein VP2
M: structural polyprotein VP2
N: structural polyprotein VP2
O: structural polyprotein VP2
P: structural polyprotein VP2
Q: structural polyprotein VP2
R: structural polyprotein VP2
S: structural polyprotein VP2
T: structural polyprotein VP2
hetero molecules

A: structural polyprotein VP2
B: structural polyprotein VP2
C: structural polyprotein VP2
D: structural polyprotein VP2
E: structural polyprotein VP2
F: structural polyprotein VP2
G: structural polyprotein VP2
H: structural polyprotein VP2
I: structural polyprotein VP2
J: structural polyprotein VP2
K: structural polyprotein VP2
L: structural polyprotein VP2
M: structural polyprotein VP2
N: structural polyprotein VP2
O: structural polyprotein VP2
P: structural polyprotein VP2
Q: structural polyprotein VP2
R: structural polyprotein VP2
S: structural polyprotein VP2
T: structural polyprotein VP2
hetero molecules

A: structural polyprotein VP2
B: structural polyprotein VP2
C: structural polyprotein VP2
D: structural polyprotein VP2
E: structural polyprotein VP2
F: structural polyprotein VP2
G: structural polyprotein VP2
H: structural polyprotein VP2
I: structural polyprotein VP2
J: structural polyprotein VP2
K: structural polyprotein VP2
L: structural polyprotein VP2
M: structural polyprotein VP2
N: structural polyprotein VP2
O: structural polyprotein VP2
P: structural polyprotein VP2
Q: structural polyprotein VP2
R: structural polyprotein VP2
S: structural polyprotein VP2
T: structural polyprotein VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,961,760108
Polymers2,959,94860
Non-polymers1,81348
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area425650 Å2
ΔGint-1245 kcal/mol
Surface area704320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)316.412, 316.412, 316.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-5501-

CL

21B-5901-

CA

31P-5502-

CL

41P-5902-

CA

51C-5905-

HOH

61K-459-

HOH

71P-5903-

HOH

81P-5904-

HOH

-
Components

#1: Protein
structural polyprotein VP2 / capsid protein VP2


Mass: 49332.461 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bursal disease virus (Gumboro virus)
Genus: Avibirnavirus / Strain: P3009 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6S9I7, UniProt: Q9WR38*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4445 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONNSRRC BL17B221.0717
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 12, 2004
ADSC QUANTUM 2102CCDJul 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.07171
ReflectionResolution: 2.6→40 Å / Num. all: 320334 / Num. obs: 318732 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 10.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 18.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.1 / Num. unique all: 30571 / % possible all: 96

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WCD

1wcd


Resolution: 2.6→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 14255 -random
Rwork0.165 ---
all0.168 320312 --
obs0.168 286954 89.6 %-
Displacement parametersBiso mean: 42.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62495 0 16 4445 66956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shellResolution: 2.6→2.69 Å
RfactorNum. reflection% reflection
Rfree0.249 1116 -
Rwork0.303 --
obs-23504 73.9 %

+
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://pdbjlvh1.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