[English] 日本語
Yorodumi
- PDB-9ygd: Asymmetric cryoEM structure of F7 pyocin tail tip in the post-eje... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ygd
TitleAsymmetric cryoEM structure of F7 pyocin tail tip in the post-ejection state
Components
  • (Phage tail protein) x 2
  • MF2 protein
  • Tail assembly protein
  • Tail hub protein of F7 pyocin
KeywordsVIRUS LIKE PARTICLE / Phage / tail / bacteriocin / Pseudomonas / cryoEM / tip / fibers
Function / homology
Function and homology information


iron-sulfur cluster binding / symbiont entry into host cell / host cell cytoplasm
Similarity search - Function
Phage tail tube protein, lambda-like / Phage tail tube, TTP, lambda-like / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Phage minor tail protein L / Phage minor tail protein / : / Tip attachment protein J,FNIII-A domain / : / Domain of unknown function DUF1983 ...Phage tail tube protein, lambda-like / Phage tail tube, TTP, lambda-like / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Phage minor tail protein L / Phage minor tail protein / : / Tip attachment protein J,FNIII-A domain / : / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber protein / Tip attachment protein J / Putative phage tail protein / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Uncharacterized protein / Tail assembly protein / Phage tail protein / Phage tail protein / MF2 protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHe, Y. / Cai, X.Y. / Li, A.S.C. / Davidson, A.R. / Zhou, Z.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI094386 United States
CitationJournal: To Be Published
Title: Atomic structures and bactericidal actions of a non-contractile tailocin against Pseudomonas aeruginosa
Authors: He, Y. / Cai, X.Y. / Li, A.S.C. / Davidson, A.R. / Zhou, Z.H.
History
DepositionSep 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 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
D: Phage tail protein
J: Tail hub protein of F7 pyocin
K: Phage tail protein
L: Tail assembly protein
M: Tail assembly protein
N: Phage tail protein
O: Phage tail protein
P: Phage tail protein
Q: Phage tail protein
R: MF2 protein
S: MF2 protein
T: Tail hub protein of F7 pyocin
U: Tail hub protein of F7 pyocin
V: MF2 protein
W: Phage tail protein
X: MF2 protein
Y: MF2 protein
Z: Phage tail protein
a: Tail assembly protein
c: Phage tail protein
d: MF2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)660,14524
Polymers659,09021
Non-polymers1,0553
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 4 types, 18 molecules DNOJTUKPQWZcRSVXYd

#1: Protein Phage tail protein


Mass: 130341.586 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A7M2ZXW7
#2: Protein Tail hub protein of F7 pyocin


Mass: 25117.746 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A3E1N7Q2
#3: Protein
Phage tail protein / VF2 protein


Mass: 17422.328 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q9R3G3
#5: Protein
MF2 protein / Phage tail protein


Mass: 12493.884 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q9S561

-
Protein/peptide / Non-polymers , 2 types, 6 molecules LMa

#4: Protein/peptide Tail assembly protein


Mass: 4405.006 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A643J512
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: F7 pyocin / Type: COMPLEX / Entity ID: #1-#2, #4-#5, #3 / Source: NATURAL
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52498 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00347499
ELECTRON MICROSCOPYf_angle_d0.53164635
ELECTRON MICROSCOPYf_dihedral_angle_d12.0117142
ELECTRON MICROSCOPYf_chiral_restr0.0437053
ELECTRON MICROSCOPYf_plane_restr0.0048616

+
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