[English] 日本語
Yorodumi
- PDB-8eao: Cryo-EM structure of the in-situ gp1-gp4 complex from bacteriopha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8eao
TitleCryo-EM structure of the in-situ gp1-gp4 complex from bacteriophage P22
Components
  • Peptidoglycan hydrolase gp4
  • Portal protein
KeywordsVIRAL PROTEIN / Bacteriophage P22
Function / homology
Function and homology information


viral DNA genome packaging, headful / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / virus tail / virion assembly / hydrolase activity
Similarity search - Function
Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein
Similarity search - Domain/homology
Portal protein / Head-to-tail adapter protein gp4
Similarity search - Component
Biological speciesSalmonella phage P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang, C. / Liu, J. / Molineux, I.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: In-situ structure of tail machine reveals mechanistic insights into P22 assembly.
Authors: Wang, C. / Liu, J. / Molineux, I.J.
History
DepositionAug 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidoglycan hydrolase gp4
B: Portal protein
C: Peptidoglycan hydrolase gp4
D: Portal protein
E: Peptidoglycan hydrolase gp4
F: Portal protein
G: Peptidoglycan hydrolase gp4
H: Portal protein
I: Peptidoglycan hydrolase gp4
J: Portal protein
K: Peptidoglycan hydrolase gp4
L: Portal protein
M: Peptidoglycan hydrolase gp4
N: Portal protein
O: Peptidoglycan hydrolase gp4
P: Portal protein
Q: Peptidoglycan hydrolase gp4
R: Portal protein
S: Peptidoglycan hydrolase gp4
T: Portal protein
U: Peptidoglycan hydrolase gp4
V: Portal protein
W: Peptidoglycan hydrolase gp4
X: Portal protein


Theoretical massNumber of molelcules
Total (without water)1,048,17224
Polymers1,048,17224
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Peptidoglycan hydrolase gp4 / Gene product 4 / Gp4 / Internal virion protein gp4 / Tail adapter protein gp4


Mass: 16231.166 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26746
#2: Protein
Portal protein / Gene product 1 / Gp1 / Head-to-tail connector


Mass: 71116.539 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26744
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cryo-EM structure of the in-situ gp1-gp4 complex from bacteriophgage P22
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella phage P22 (virus)
Buffer solutionpH: 7.5
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: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73420 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00373140
ELECTRON MICROSCOPYf_angle_d0.51999192
ELECTRON MICROSCOPYf_dihedral_angle_d3.8629828
ELECTRON MICROSCOPYf_chiral_restr0.04110716
ELECTRON MICROSCOPYf_plane_restr0.00313116

+
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