[English] 日本語
Yorodumi
- PDB-7boz: N-teminal of mature bacteriophage T7 tail fiber protein gp17 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7boz
TitleN-teminal of mature bacteriophage T7 tail fiber protein gp17
ComponentsN-teminal of mature bacteriophage T7 tail fiber protein gp17
KeywordsSTRUCTURAL PROTEIN / phage / portal / protein / mature
Function / homology
Function and homology information


virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / identical protein binding
Similarity search - Function
: / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein
Similarity search - Domain/homology
Biological speciesEscherichia phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChen, W.Y. / Xiao, H.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: Protein Cell / Year: 2020
Title: Structural changes of a bacteriophage upon DNA packaging and maturation.
Authors: Wenyuan Chen / Hao Xiao / Xurong Wang / Shuanglin Song / Zhen Han / Xiaowu Li / Fan Yang / Li Wang / Jingdong Song / Hongrong Liu / Lingpeng Cheng /
History
DepositionMar 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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-30137
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-30137
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
a: N-teminal of mature bacteriophage T7 tail fiber protein gp17
b: N-teminal of mature bacteriophage T7 tail fiber protein gp17
c: N-teminal of mature bacteriophage T7 tail fiber protein gp17
d: N-teminal of mature bacteriophage T7 tail fiber protein gp17
e: N-teminal of mature bacteriophage T7 tail fiber protein gp17
f: N-teminal of mature bacteriophage T7 tail fiber protein gp17
g: N-teminal of mature bacteriophage T7 tail fiber protein gp17
h: N-teminal of mature bacteriophage T7 tail fiber protein gp17
i: N-teminal of mature bacteriophage T7 tail fiber protein gp17
j: N-teminal of mature bacteriophage T7 tail fiber protein gp17
k: N-teminal of mature bacteriophage T7 tail fiber protein gp17
l: N-teminal of mature bacteriophage T7 tail fiber protein gp17
m: N-teminal of mature bacteriophage T7 tail fiber protein gp17
n: N-teminal of mature bacteriophage T7 tail fiber protein gp17
o: N-teminal of mature bacteriophage T7 tail fiber protein gp17
p: N-teminal of mature bacteriophage T7 tail fiber protein gp17
q: N-teminal of mature bacteriophage T7 tail fiber protein gp17
r: N-teminal of mature bacteriophage T7 tail fiber protein gp17


Theoretical massNumber of molelcules
Total (without water)1,109,55418
Polymers1,109,55418
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area33830 Å2
ΔGint-241 kcal/mol
Surface area130160 Å2

-
Components

#1: Protein
N-teminal of mature bacteriophage T7 tail fiber protein gp17 / Gene product 17 / Gp17 / Tail fiber protein gp17


Mass: 61641.875 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T7 (virus) / Gene: 17 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03748

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: N-teminal of mature bacteriophage T7 tail fiber protein gp17
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia phage T7 (virus)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 24 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55212 / 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