[English] 日本語
Yorodumi
- PDB-11xb: Cryo-EM of Hxc endopilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 11xb
TitleCryo-EM of Hxc endopilus
ComponentsType II secretion system core protein G
KeywordsPROTEIN FIBRIL / endopilus / cryo-EM / Hxc
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane
Similarity search - Function
Type II secretion system protein GspG / Type II secretion system protein GspG, C-terminal / Type II secretion system (T2SS), protein G / Bacterial general secretion pathway protein G-type pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Type II secretion system core protein G
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSonani, R.R. / Ball, G. / Chouikha, I. / Durand, E. / Voulhoux, R. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Structure / Year: 2026
Title: Structures of the Xcp and Hxc T2SS endopili provide new insights into type IV pili subfamilies.
Authors: Ravi R Sonani / Iman Chouikha / Geneviève Ball / Mathilde Tribout / Edward H Egelman / Romé Voulhoux /
Abstract: Type IV filaments (T4F) are widespread bacterial appendages involved in adhesion, motility, DNA uptake, and protein secretion. In the type II secretion system (T2SS), a short pilus-like structure ...Type IV filaments (T4F) are widespread bacterial appendages involved in adhesion, motility, DNA uptake, and protein secretion. In the type II secretion system (T2SS), a short pilus-like structure termed the endopilus drives protein export across the outer membrane. Despite its important function, the specific molecular determinants of endopili remain poorly understood. Here, we used cryo-electron microscopy to determine the structures of two endopili assembled by the independent Hxc and Xcp T2SS systems of Pseudomonas aeruginosa. Comparative analyses reveal defining structural and chemical features of T2SS endopili, including a unique surface property of the XcpG endopilus that explains its distinctive bundling behavior. Mapping inter-subunit interactions further identifies residues governing selective assembly within coexisting secretion systems. Comparisons with related type IVa pili define a conserved architectural framework and constrained helical parameters characteristic of the T2SS endopilus family, providing insight into how subtle chemical variations encode functional specificity and efficient protein export.
History
DepositionMar 17, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 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
B: Type II secretion system core protein G
C: Type II secretion system core protein G
D: Type II secretion system core protein G
E: Type II secretion system core protein G
F: Type II secretion system core protein G
G: Type II secretion system core protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,89812
Polymers85,6576
Non-polymers2406
Water00
1


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

-
Components

#1: Protein
Type II secretion system core protein G / General secretion pathway protein G


Mass: 14276.233 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0681 / Production host: Pseudomonas aeruginosa PAK (bacteria) / References: UniProt: Q9I5P4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Hxc endo pilus filament / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Source (recombinant)Organism: Pseudomonas aeruginosa PAK (bacteria)
Buffer solutionpH: 7
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: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.16_3549model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 10.37 ° / Axial rise/subunit: 83.2 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42709 / Symmetry type: HELICAL

+
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