[English] 日本語
Yorodumi
- PDB-9mt4: Connector structure of phage JohannRWettstein (Bas63) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mt4
TitleConnector structure of phage JohannRWettstein (Bas63)
Components
  • (Phage protein) x 2
  • Collar protein
  • Head-closure protein
  • Portal protein
  • Structural protein
  • Tail terminator protein
  • Tube protein
KeywordsVIRAL PROTEIN / connector / portal / adaptor / head completion / tail terminator / fiber / whisker / collar / tube / sheath / phage / bacteriophage / neck / Bas63 / JohannRWettstein
Function / homology
Function and homology information


: / Phage neck terminator protein / Protein of unknown function DUF935 / Portal protein of Mu bacteriophage / Structural protein ORF10, bacteriophage KPP10 / Protein of unknown function DUF3383 / Bacteriophage PhiTE tail tube protein / Protein of unknown function (DUF3383)
Similarity search - Domain/homology
Uncharacterized protein / Phage neck terminator protein gp12-like domain-containing protein / Head-closure protein / Uncharacterized protein / Portal protein / Structural protein / Phage protein / Phage protein
Similarity search - Component
Biological speciesEscherichia phage JohannRWettstein (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHodgkinson-Bean, J.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
CitationJournal: Sci Adv / Year: 2025
Title: C12 local connector reconstruction of phage JohannRWettstein (Bas63)
Authors: Hodgkinson-Bean, J. / Ayala, R. / McJarrow-Keller, K. / Cassin, L. / Rutter, G.L. / Crowe, A.J.M. / Wolf, M. / Bostina, M.
History
DepositionJan 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Portal protein
A: Portal protein
E: Head-closure protein
F: Tail terminator protein
P: Tube protein
O: Tube protein
I: Phage protein
J: Phage protein
L: Phage protein
K: Phage protein
M: Phage protein
N: Phage protein
Q: Structural protein
R: Structural protein
C: Phage protein
D: Phage protein
G: Collar protein
H: Collar protein


Theoretical massNumber of molelcules
Total (without water)419,65918
Polymers419,65918
Non-polymers00
Water00
1
B: Portal protein
A: Portal protein
E: Head-closure protein
F: Tail terminator protein
P: Tube protein
O: Tube protein
I: Phage protein
J: Phage protein
L: Phage protein
K: Phage protein
M: Phage protein
N: Phage protein
Q: Structural protein
R: Structural protein
C: Phage protein
D: Phage protein
G: Collar protein
H: Collar protein
x 6


Theoretical massNumber of molelcules
Total (without water)2,517,954108
Polymers2,517,954108
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

-
Components

-
Protein , 8 types, 18 molecules BAEFPOIJLKMNQRCDGH

#1: Protein Portal protein


Mass: 55447.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VVG7
#2: Protein Head-closure protein


Mass: 15630.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VV34
#3: Protein Tail terminator protein


Mass: 22316.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VUU6
#4: Protein Tube protein


Mass: 16203.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VV62
#5: Protein
Phage protein


Mass: 11673.070 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VWD1
#6: Protein Structural protein


Mass: 48916.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VVP5
#7: Protein Phage protein


Mass: 16980.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE8B2G2
#8: Protein Collar protein


Mass: 18289.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VUQ8

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: JohannRWettstein (Bas63) / Type: VIRUS
Details: Connector structure of phage JohannRWettstein (Bas63).
Source: NATURAL
Source (natural)Organism: JohannRWettstein (Bas63) (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7.4 / Details: Phage buffer
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris HCL 7.41
210 mMmagnesium sulphateMgSO41
30.01 % W/VGelatin1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Mature viral particles with packaged genomes
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 49.6 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20388 / 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