[English] 日本語
Yorodumi
- PDB-9lu5: Structure of bacteriophage T4 neck protein gp13 and gp14 and Hfq ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lu5
TitleStructure of bacteriophage T4 neck protein gp13 and gp14 and Hfq assembled in vitro in C6 symmetry
Components
  • Neck protein gp13
  • Neck protein gp14
  • RNA-binding protein Hfq
KeywordsVIRAL PROTEIN / Structural protein
Function / homology
Function and homology information


regulation of translation, ncRNA-mediated / regulation of RNA stability / virion component / regulation of DNA-templated transcription / RNA binding / cytosol
Similarity search - Function
Bacteriophage T4, Gp14, neck protein / Virus neck protein / RNA-binding protein Hfq / Hfq protein / : / Sm domain profile. / LSM domain superfamily
Similarity search - Domain/homology
RNA-binding protein Hfq / Neck protein gp13 / Neck protein gp14
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsHan, L. / Mao, Q. / Sun, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of bacteriophage T4 neck protein gp13 and gp14 and Hfq assembled in vitro in C6 symmetry
Authors: Han, L. / Mao, Q. / Sun, L.
History
DepositionFeb 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Neck protein gp13
I: Neck protein gp13
G: Neck protein gp13
T: RNA-binding protein Hfq
S: RNA-binding protein Hfq
X: RNA-binding protein Hfq
W: RNA-binding protein Hfq
V: RNA-binding protein Hfq
U: RNA-binding protein Hfq
O: Neck protein gp14
N: Neck protein gp14
M: Neck protein gp14
R: Neck protein gp14
Q: Neck protein gp14
P: Neck protein gp14
E: Neck protein gp13
A: Neck protein gp13
B: Neck protein gp13
D: Neck protein gp13
F: Neck protein gp13
H: Neck protein gp13
J: Neck protein gp13
K: Neck protein gp13
L: Neck protein gp13


Theoretical massNumber of molelcules
Total (without water)686,66424
Polymers686,66424
Non-polymers00
Water00
1


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

-
Components

#1: Protein
Neck protein gp13 / Gene product 13 / gp13


Mass: 35601.078 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Escherichia phage T4 is not available during the biocuration, replaced by P11110 temporarily.
Source: (gene. exp.) Escherichia phage T4 (virus) / Gene: 13 / Production host: Escherichia coli (E. coli) / References: UniProt: P11110
#2: Protein
RNA-binding protein Hfq


Mass: 12583.903 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Escherichia phage T4 is not available during the biocuration, replaced by A7ZV41 temporarily.
Source: (gene. exp.) Escherichia phage T4 (virus) / Gene: hfq, EcE24377A_4730 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZV41
#3: Protein
Neck protein gp14 / Gene product 14 / gp14


Mass: 30657.924 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Escherichia phage T4 is not available during the biocuration, replaced by P11111 temporarily.
Source: (gene. exp.) Escherichia phage T4 (virus) / Gene: 14 / Production host: Escherichia coli (E. coli) / References: UniProt: P11111
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Complex of bacteriophage T4 neck protein gp13 and gp14 and Hfq assembled in vitro
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia phage T4 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.17.1_3660model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 381536 / 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