[English] 日本語
Yorodumi
- PDB-8jww: top segment of the bacteriophage M13 mini variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jww
Titletop segment of the bacteriophage M13 mini variant
Components
  • Capsid protein G8P
  • Tail virion protein G7P
  • Tail virion protein G9P
KeywordsVIRAL PROTEIN / M13
Function / homology
Function and homology information


helical viral capsid / host cell membrane / virion component / host cell plasma membrane / membrane
Similarity search - Function
Tail virion protein G7P / Tail virion protein G7P / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P
Similarity search - Domain/homology
Tail virion protein G7P / Tail virion protein G9P / Capsid protein G8P
Similarity search - Component
Biological speciesEnterobacteria phage M13 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsXiang, Y. / Jia, Q.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of a bacteriophage M13 mini variant
Authors: Xiang, Y. / Jia, Q.
History
DepositionJun 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Z: Capsid protein G8P
B: Capsid protein G8P
C: Capsid protein G8P
D: Tail virion protein G9P
E: Capsid protein G8P
F: Tail virion protein G7P
H: Capsid protein G8P
A: Capsid protein G8P
G: Capsid protein G8P
I: Capsid protein G8P
J: Tail virion protein G9P
K: Capsid protein G8P
L: Tail virion protein G7P
M: Capsid protein G8P
N: Capsid protein G8P
O: Capsid protein G8P
P: Capsid protein G8P
Q: Tail virion protein G9P
R: Capsid protein G8P
S: Tail virion protein G7P
T: Capsid protein G8P
V: Capsid protein G8P
W: Capsid protein G8P
X: Capsid protein G8P
Y: Tail virion protein G9P
AA: Capsid protein G8P
BA: Tail virion protein G7P
CA: Capsid protein G8P
DA: Capsid protein G8P
EA: Capsid protein G8P
FA: Capsid protein G8P
GA: Tail virion protein G9P
HA: Capsid protein G8P
IA: Tail virion protein G7P
JA: Capsid protein G8P


Theoretical massNumber of molelcules
Total (without water)167,36835
Polymers167,36835
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein/peptide ...
Capsid protein G8P / Coat protein B / Gene 8 protein / G8P / M13 procoat / Major coat protein


Mass: 5243.014 Da / Num. of mol.: 25
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage M13 (virus) / Gene: VIII / Production host: Escherichia (bacteria) / References: UniProt: P69541
#2: Protein/peptide
Tail virion protein G9P / Coat protein C / polypeptide II / G9P


Mass: 3655.270 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage M13 (virus) / Gene: IX / Production host: Escherichia (bacteria) / References: UniProt: P69538
#3: Protein/peptide
Tail virion protein G7P / Coat protein C / polypeptide I / Gene 7 protein / G7P


Mass: 3603.215 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage M13 (virus) / Gene: VII / Production host: Escherichia (bacteria) / References: UniProt: P69535

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: top segment of the bacteriophage M13 mini variant / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Enterobacteria phage M13 (virus)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 / Nominal defocus max: 1700 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20910 / 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