[English] 日本語
Yorodumi
- PDB-3jb5: Capsid Structure of the Propionibacterium acnes Bacteriophage ATC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jb5
TitleCapsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear
Componentsmajor capsid protein
KeywordsVIRUS / acne / bacteriophage / HK97-like
Function / homologyGp6
Function and homology information
Biological speciesPropionibacterium phage PA6 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsChiou, J. / Zhang, X. / Marinelli, L.J. / Modlin, R.L. / Zhou, Z.H.
CitationJournal: To be Published
Title: Capsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear
Authors: Chiou, J. / Zhang, X. / Marinelli, L.J. / Modlin, R.L. / Zhou, Z.H.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

-
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-6398
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6398
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein


Theoretical massNumber of molelcules
Total (without water)229,3567
Polymers229,3567
Non-polymers00
Water00
1
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)13,761,334420
Polymers13,761,334420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein
x 5


  • icosahedral pentamer
  • 1.15 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,146,77835
Polymers1,146,77835
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.38 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,376,13342
Polymers1,376,13342
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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


Mass: 32765.082 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Propionibacterium phage PA6 (virus) / References: UniProt: A4K473

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Propionibacterium acnes bacteriophage ATCC_Clear / Type: VIRUS
Molecular weightValue: 33 MDa / Experimental value: YES
Details of virusEmpty: NO / Enveloped: NO / Host category: BACTERIA(EUBACTERIA) / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Propionibacterium acnes / Strain: 6919
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Purified sample was applied to a Quantifoil grid.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 15 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Method: Blot for 15 seconds before plunging

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 16, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38462 X / Calibrated magnification: 38462 X / Nominal defocus max: 2270 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 3168
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: FREALIGN / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27504 / Nominal pixel size: 1.3 Å / Actual pixel size: 1.3 Å
Details: (Single particle details: The particles were selected using an in-house selection procedure.) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms15232 0 0 0 15232

+
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