[English] 日本語
Yorodumi
- PDB-3iyj: Bovine papillomavirus type 1 outer capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iyj
TitleBovine papillomavirus type 1 outer capsid
ComponentsMajor capsid protein L1
KeywordsVIRUS / bovine papillomavirus BPV1 / major capsid protein L1 / single particle cryo-EM / high resolution / Capsid protein / Late protein / Virion
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell
Similarity search - Function
Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein L1
Similarity search - Component
Biological speciesBovine papillomavirus type 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWolf, M. / Garcea, R.L. / Grigorieff, N. / Harrison, S.C.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Subunit interactions in bovine papillomavirus.
Authors: Matthias Wolf / Robert L Garcea / Nikolaus Grigorieff / Stephen C Harrison /
Abstract: Papillomaviruses, members of a group of dsDNA viruses associated with epithelial growths and tumors, have compact capsids assembled from 72 pentamers of the protein L1. We have determined the ...Papillomaviruses, members of a group of dsDNA viruses associated with epithelial growths and tumors, have compact capsids assembled from 72 pentamers of the protein L1. We have determined the structure of bovine papillomavirus by electron cryomicrosopy (cryoEM), at approximately 3.6 A resolution. The density map, obtained from single-particle analysis of approximately 4,000 particle images, shows the trace of the L1 polypeptide chain and reveals how the N- and C-terminal "arms" of a subunit (extensions from its beta-jelly-roll core) associate with a neighboring pentamer. Critical contacts come from the C-terminal arm, which loops out from the core of the subunit, forms contacts (including a disulfide) with two subunits in a neighboring pentamer, and reinserts into the pentamer from which it emanates. This trace corrects one feature of an earlier model. We discuss implications of the structure for virion assembly and for pathways of infectious viral entry. We suggest that it should be possible to obtain image reconstructions of comparable resolution from cryoEM images of asymmetric particles. From the work on papillomavirus described here, we estimate that such a reconstruction will require about 1.5 million images to achieve the same number of averaged asymmetric units; structural variability will increase this number substantially.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5155
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5156
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5155
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-5156
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Major capsid protein L1
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)333,7146
Polymers333,7146
Non-polymers00
Water0
1
F: Major capsid protein L1
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
x 60


Theoretical massNumber of molelcules
Total (without water)20,022,848360
Polymers20,022,848360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
F: Major capsid protein L1
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
x 5


  • icosahedral pentamer
  • 1.67 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,668,57130
Polymers1,668,57130
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
F: Major capsid protein L1
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
x 6


  • icosahedral 23 hexamer
  • 2 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)2,002,28536
Polymers2,002,28536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein
Major capsid protein L1


Mass: 55619.023 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: BPV was purified from cow warts on a CsCl gradient (Li et al (1998) J Virol 72: 2160-2167)
Source: (natural) Bovine papillomavirus type 1 / Strain: BPV type 1 / References: UniProt: P03103

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: BOVINE PAPILLOMAVIRUS TYPE 1 (BPV1), FULL VIRION / Type: VIRUS
Details of virusHost category: VERTEBRATES / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Bos taurus
Buffer solutionName: 20MM TRIS PH 6.2, 100MM NACL, 0.5MM CACL2 / pH: 6.2 / Details: 20MM TRIS PH 6.2, 100MM NACL, 0.5MM CACL2
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: C-FLAT CF-1/2-4C
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: VITRIFICATION CARRIED OUT IN COLD ROOM.

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Dec 7, 2008 / Details: OBJ APERTURE CUTOFF AT 2.4A
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 56588 X / Nominal defocus max: 2900 nm / Nominal defocus min: 1800 nm / Cs: 2 mm
Specimen holderTemperature: 77 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 49

-
Processing

EM software
IDNameCategory
1CNSmodel fitting
2FREALIGN3D reconstruction
CTF correctionDetails: CTFILT3 WITH INDIVIDUAL PARTICLE ADJUSTMENT
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CENTRAL SECTIONS / Resolution: 4.2 Å / Num. of particles: 3997 / Nominal pixel size: 1.186 Å / Actual pixel size: 1.237 Å
Magnification calibration: ATOMIC PENTAMER MODEL, MAXIMIZED REAL-SPACE CORRELATION USING SITUS
Details: EWALD SPHERE CORRECTION / Symmetry type: POINT
Atomic model buildingB value: 131 / Protocol: RIGID BODY FIT / Space: RECIPROCAL
Target criteria: MLHL TARGET WITH AMPL. AND PHASE PROBABILITY DISTRIBUTION
Details: METHOD--RIGID BODY DOCKING, THEN COORDINATE REFINEMENT IN CNS REFINEMENT PROTOCOL--SEE 3D-FITTING DETAILS
Atomic model buildingPDB-ID: 1DZL

1dzl


Details: HOMOLOGY MODEL 1DZL
RefinementHighest resolution: 4.2 Å
Displacement parametersBaniso 11: 131 Å2
Refinement stepCycle: LAST / Highest resolution: 4.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22614 0 0 0 22614

+
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