[English] 日本語
Yorodumi
- PDB-11lc: Bacteriophage Goslar Collar -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 11lc
TitleBacteriophage Goslar Collar
Components
  • Tail Adaptor Protein gp50 NTD
  • Tail Terminator protein gp51
  • Tail Tube of Bacteriophage Goslar
  • Tail sheath protein gp29 gp29PR domain-containing protein
  • Whiskers Protein gp126
KeywordsVIRAL PROTEIN / Collar / WAC / Whiskers
Function / homology
Function and homology information


: / : / Putative phage head-tail joining protein / Phage head to tail associated domain / : / Phage tail tube protein / : / Bacteriophage phiKZ, gp29PR
Similarity search - Domain/homology
Uncharacterized protein / Virion structural protein / Tail sheath protein gp29 gp29PR domain-containing protein
Similarity search - Component
Biological speciesGoslarvirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsBasu, D. / Gu, Y. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Emerging Pathogens Initiative United States
CitationJournal: To Be Published
Title: Bacteriophage Goslar Collar
Authors: Basu, D.
History
DepositionMar 2, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AJ: Tail Tube of Bacteriophage Goslar
AY: Tail Tube of Bacteriophage Goslar
Ah: Tail sheath protein gp29 gp29PR domain-containing protein
Ao: Tail Adaptor Protein gp50 NTD
Ap: Tail Adaptor Protein gp50 NTD
D: Tail Terminator protein gp51
M: Whiskers Protein gp126
N: Whiskers Protein gp126
O: Whiskers Protein gp126
P: Whiskers Protein gp126
Q: Whiskers Protein gp126
h: Whiskers Protein gp126
i: Whiskers Protein gp126
j: Whiskers Protein gp126
k: Whiskers Protein gp126
l: Whiskers Protein gp126


Theoretical massNumber of molelcules
Total (without water)672,69716
Polymers672,69716
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Tail Tube of Bacteriophage Goslar


Mass: 32990.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Goslarvirus / References: UniProt: A0A482GE68
#2: Protein Tail sheath protein gp29 gp29PR domain-containing protein


Mass: 76777.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Goslarvirus / References: UniProt: A0A482GKT6
#3: Protein Tail Adaptor Protein gp50 NTD


Mass: 49920.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Goslarvirus / References: UniProt: A0A482GGR9
#4: Protein Tail Terminator protein gp51


Mass: 60014.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Goslarvirus
#5: Protein
Whiskers Protein gp126


Mass: 37008.445 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Goslarvirus
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Goslarvirus / Type: VIRUS / Entity ID: #5, #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Goslarvirus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

-
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: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
13cryoSPARC4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32008 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

+
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