[English] 日本語
Yorodumi
- PDB-3jvb: Crystal structure of infectious baculovirus polyhedra -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jvb
TitleCrystal structure of infectious baculovirus polyhedra
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / Jelly-roll / disulfide bond / domain swapping
Function / homologyPolyhedrin / Polyhedrin / viral occlusion body / structural molecule activity / Polyhedrin
Function and homology information
Biological speciesWiseana signata NPV (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsCoulibaly, F. / Chiu, E. / Metcalf, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The atomic structure of baculovirus polyhedra reveals the independent emergence of infectious crystals in DNA and RNA viruses
Authors: Coulibaly, F. / Chiu, E. / Gutmann, S. / Rajendran, C. / Haebel, P.W. / Ikeda, K. / Mori, H. / Ward, V.K. / Schulze-Briese, C. / Metcalf, P.
History
DepositionSep 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8022
Polymers28,7061
Non-polymers961
Water1,54986
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)345,62324
Polymers344,47012
Non-polymers1,15312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area62440 Å2
ΔGint-443 kcal/mol
Surface area109170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.437, 102.437, 102.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-244-

SO4

21A-244-

SO4

DetailsPOLYHEDRA ARE VIRUS-CONTAINING CRYSTALS, WHICH REPRESENT THE MAIN INFECTIOUS FORM OF BACULOVIRUS. THE BIOLOGICAL ASSEMBLY IS THE WHOLE CRYSTAL. DODECAMERS OF THE POLYHEDRIN PROTEIN ARE PUTATIVE BUILDING BLOCKS OF THE CRYSTAL. INTERFACES INVOLVED IN GENERATING BIOMOLECULES 2-7 EXIST IN THE CRYSTAL BUT MAY NOT BE RELEVANT IN SOLUTION.

-
Components

#1: Protein Polyhedrin


Mass: 28705.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Crystals were directly purified from insects (larvae of porina moths) naturally infected by a baculovirus (Wiseana spp. nucleopolyhedrosis virus)
Source: (natural) Wiseana signata NPV (virus) / References: UniProt: O37157
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 19

-
Sample preparation

CrystalDensity Matthews: 1.560221 Å3/Da / Density % sol: 21.164995 %
Crystal growTemperature: 300 K / pH: 7
Details: Natural intracellular Crystals were directly purified from larvae of porina moths infected by a baculovirus (WNPV), pH 7, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2009 / Details: MD2 DIFFRACTOMETER
RadiationMonochromator: SAGITALLY HORIZONTAL FOCUSSING SI(111) MERIDIONALLY VERTICAL FOCUSSING RH-COATED MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→30 Å / Num. obs: 9646 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 15 % / Biso Wilson estimate: 21.21 Å2 / Rmerge(I) obs: 0.349 / Net I/σ(I): 8
Reflection shellResolution: 2.17→2.29 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SHARPphasing
BUSTER2.8.0refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JW6

3jw6


Resolution: 2.17→20.91 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.33 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residue ACys131 forms a disulfide bond with residue BCys131 of symmetry molecule 4566. By symmetry, this also implies that residue BCys131 forms a disulfide bond with residue ACys131 of symmetry molecule 4566.
RfactorNum. reflection% reflectionSelection details
Rfree0.1899 947 9.84 %RANDOM
Rwork0.1612 ---
obs0.164 9620 99.7 %-
Displacement parametersBiso max: 114 Å2 / Biso mean: 21.582 Å2 / Biso min: 5.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.198 Å
Refinement stepCycle: LAST / Resolution: 2.17→20.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 5 86 1710
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_dihedral_angle_d18.26
X-RAY DIFFRACTIONo_angle_deg1.04
LS refinement shellResolution: 2.17→2.43 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2244 274 10.14 %
Rwork0.1905 2428 -
all0.194 2702 -
obs--99.9 %

+
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://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