[English] 日本語
Yorodumi
- PDB-9qgl: Cryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qgl
TitleCryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6), in extended state
Components
  • (Phage tail protein) x 2
  • (Phage tail sheath family ...) x 3
  • (Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment ...) x 2
  • Baseplate protein J-like domain-containing protein
  • Contractile injection system tube protein N-terminal domain-containing protein
KeywordsVIRUS LIKE PARTICLE / Contractile injection system
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain ...Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Phage tail protein / Contractile injection system tube protein N-terminal domain-containing protein / Phage tail sheath family protein / Phage tail sheath family protein / Baseplate protein J-like domain-containing protein / Phage tail sheath family protein / Phage tail protein / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17 / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsMarin-Arraiza, L. / Taylor, N.M.I.
Funding support Denmark, Spain, 5items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Novo Nordisk FoundationNNF17OC0031006 Denmark
Novo Nordisk FoundationNNF23OC0081528 Denmark
LundbeckfondenR434-2023-289 Denmark
La Caixa FoundationLCF/BQ/EU21/11890147 Spain
CitationJournal: Nat Commun / Year: 2025
Title: Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states
Authors: Marin-Arraiza, L. / Roa-Eguiara, A. / Pape, T. / Sofos, N. / Hendriks, I.A. / Lund Nielsen, M. / Steiner-Rebrova, E.M. / Taylor, N.M.I.
History
DepositionMar 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1A: Phage tail protein
1B: Phage tail protein
1C: Phage tail protein
1D: Phage tail protein
1E: Phage tail protein
1F: Phage tail protein
2A: Phage tail sheath family protein
2B: Phage tail sheath family protein
2C: Phage tail sheath family protein
2D: Phage tail sheath family protein
2E: Phage tail sheath family protein
2F: Phage tail sheath family protein
5A: Phage tail protein
5B: Phage tail protein
5C: Phage tail protein
5D: Phage tail protein
5E: Phage tail protein
5F: Phage tail protein
7A: Contractile injection system tube protein N-terminal domain-containing protein
7B: Contractile injection system tube protein N-terminal domain-containing protein
7C: Contractile injection system tube protein N-terminal domain-containing protein
7D: Contractile injection system tube protein N-terminal domain-containing protein
7E: Contractile injection system tube protein N-terminal domain-containing protein
7F: Contractile injection system tube protein N-terminal domain-containing protein
9A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
9B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
9C: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
9D: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
9E: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
9F: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
C: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
D: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
E: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
F: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
a: Baseplate protein J-like domain-containing protein
b: Baseplate protein J-like domain-containing protein
c: Baseplate protein J-like domain-containing protein
d: Baseplate protein J-like domain-containing protein
e: Baseplate protein J-like domain-containing protein
f: Baseplate protein J-like domain-containing protein
3A: Phage tail sheath family protein
3B: Phage tail sheath family protein
3C: Phage tail sheath family protein
3D: Phage tail sheath family protein
3E: Phage tail sheath family protein
3F: Phage tail sheath family protein
4A: Phage tail sheath family protein
4B: Phage tail sheath family protein
4C: Phage tail sheath family protein
4D: Phage tail sheath family protein
4E: Phage tail sheath family protein
4F: Phage tail sheath family protein


Theoretical massNumber of molelcules
Total (without water)2,595,09554
Polymers2,595,09554
Non-polymers00
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, 24 molecules 1A1B1C1D1E1F5A5B5C5D5E5F7A7B7C7D7E7Fabcdef

#1: Protein
Phage tail protein


Mass: 16574.574 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc1 - tube protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18090 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JSR5
#3: Protein
Phage tail protein


Mass: 17178.578 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc5 - tube protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: C6H66_14800 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S8PZE9
#4: Protein
Contractile injection system tube protein N-terminal domain-containing protein


Mass: 24840.080 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc7 - tube initiator protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: C6H66_14790 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S8PZG1
#7: Protein
Baseplate protein J-like domain-containing protein


Mass: 110905.555 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc12 - baseplate protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18145 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JN06

-
Phage tail sheath family ... , 3 types, 18 molecules 2A2B2C2D2E2F3A3B3C3D3E3F4A4B4C4D4E4F

#2: Protein
Phage tail sheath family protein


Mass: 39009.828 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc2 - sheath protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18095 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JN00
#8: Protein
Phage tail sheath family protein


Mass: 51330.875 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc3 - sheath protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JMV2
#9: Protein
Phage tail sheath family protein


Mass: 44076.059 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc4 - sheath initiator protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18105 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JN29

-
Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment ... , 2 types, 12 molecules 9A9B9C9D9E9FABCDEF

#5: Protein
Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17


Mass: 27145.588 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc9 - sheath adaptor protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: plu1722 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MB49
#6: Protein
Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17


Mass: 101454.625 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc11 - baseplate protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: plu1720 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N649

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: PlPVC baseplate (C6) in extended state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionDetails: Patch CTF Estimation in cryoSPARC, fit local CTF to micrograph, including tilted, bent, deformed samples
Type: NONE
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53537 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002175026
ELECTRON MICROSCOPYf_angle_d0.443238530
ELECTRON MICROSCOPYf_dihedral_angle_d4.1223234
ELECTRON MICROSCOPYf_chiral_restr0.04126844
ELECTRON MICROSCOPYf_plane_restr0.00430936

+
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