[English] 日本語
Yorodumi
- PDB-6wkk: Phage G gp27 major capsid proteins and gp26 decoration proteins -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wkk
TitlePhage G gp27 major capsid proteins and gp26 decoration proteins
Components
  • Gp26 capsid decoration protein
  • Gp27 major capsid protein
KeywordsVIRUS / phage G / major capsid protein / decoration protein / capsid / icosahedral / gp26 / gp27
Function / homology: / Phage capsid / Phage capsid family / Gp26 / Gp27
Function and homology information
Biological speciesBacillus virus G
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsMonroe, L. / Gonzalez, B. / Jiang, W. / Kihara, D.
CitationJournal: J Mol Biol / Year: 2020
Title: Phage G Structure at 6.1 Å Resolution, Condensed DNA, and Host Identity Revision to a Lysinibacillus.
Authors: Brenda González / Lyman Monroe / Kunpeng Li / Rui Yan / Elena Wright / Thomas Walter / Daisuke Kihara / Susan T Weintraub / Julie A Thomas / Philip Serwer / Wen Jiang /
Abstract: Phage G has the largest capsid and genome of any known propagated phage. Many aspects of its structure, assembly, and replication have not been elucidated. Herein, we present the dsDNA-packed and ...Phage G has the largest capsid and genome of any known propagated phage. Many aspects of its structure, assembly, and replication have not been elucidated. Herein, we present the dsDNA-packed and empty phage G capsid at 6.1 and 9 Å resolution, respectively, using cryo-EM for structure determination and mass spectrometry for protein identification. The major capsid protein, gp27, is identified and found to share the HK97-fold universally conserved in all previously solved dsDNA phages. Trimers of the decoration protein, gp26, sit on the 3-fold axes and are thought to enhance the interactions of the hexameric capsomeres of gp27, for other phages encoding decoration proteins. Phage G's decoration protein is longer than what has been reported in other phages, and we suspect the extra interaction surface area helps stabilize the capsid. We identified several additional capsid proteins, including a candidate for the prohead protease responsible for processing gp27. Furthermore, cryo-EM reveals a range of partially full, condensed DNA densities that appear to have no contact with capsid shell. Three analyses confirm that the phage G host is a Lysinibacillus, and not Bacillus megaterium: identity of host proteins in our mass spectrometry analyses, genome sequence of the phage G host, and host range of phage G.
History
DepositionApr 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-21695
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-21695
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gp27 major capsid protein
B: Gp27 major capsid protein
C: Gp27 major capsid protein
D: Gp27 major capsid protein
E: Gp27 major capsid protein
F: Gp27 major capsid protein
G: Gp26 capsid decoration protein
H: Gp26 capsid decoration protein
I: Gp26 capsid decoration protein
J: Gp26 capsid decoration protein
K: Gp26 capsid decoration protein
L: Gp26 capsid decoration protein
M: Gp26 capsid decoration protein
N: Gp26 capsid decoration protein
O: Gp26 capsid decoration protein
P: Gp26 capsid decoration protein
Q: Gp26 capsid decoration protein
R: Gp26 capsid decoration protein
S: Gp26 capsid decoration protein
T: Gp26 capsid decoration protein
U: Gp26 capsid decoration protein
V: Gp26 capsid decoration protein
W: Gp26 capsid decoration protein
X: Gp26 capsid decoration protein


Theoretical massNumber of molelcules
Total (without water)469,63324
Polymers469,63324
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Gp27 major capsid protein


Mass: 30981.451 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bacillus virus G / References: UniProt: G3MB97
#2: Protein
Gp26 capsid decoration protein


Mass: 15763.595 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Bacillus virus G / References: UniProt: G3MB96

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Bacillus virus G / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacillus virus G
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Virus shellDiameter: 1600 nm / Triangulation number (T number): 52
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: In brief, phage G was grown in agarose overlays, concentrated by centrifugal pelleting and subjected to rate zonal centrifugation in a sucrose gradient. After recovery from the gradient, ...Details: In brief, phage G was grown in agarose overlays, concentrated by centrifugal pelleting and subjected to rate zonal centrifugation in a sucrose gradient. After recovery from the gradient, phage G was stored in 0.01 M Tris-Cl (pH 7.4), 0.01 M MgSO4, 6% polyethylene glycol MW 3350.
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 65 % / Chamber temperature: 298 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 14.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 375

-
Processing

EM software
IDNameCategoryDetails
1EMAN2particle selectione2boxer.py
2jsprparticle selectionbatchboxer.py
5jsprCTF correction
10jsprinitial Euler assignment
11jsprfinal Euler assignment
13jspr3D reconstruction
14MDFFmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2564
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2564
Details: Phage G's capsid was reconstructed with icosahedral symmetry
Symmetry type: POINT

+
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