[English] 日本語
Yorodumi
- EMDB-75832: Cryo-EM of T2SS OutG pilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75832
TitleCryo-EM of T2SS OutG pilus
Map data
Sample
  • Complex: OutG T2SS filament
    • Protein or peptide: Type II secretion system core protein G
  • Ligand: CALCIUM ION
KeywordsEndopilus / T2SS / PROTEIN FIBRIL
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / protein processing / 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 speciesDickeya dadantii (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSonani RR / Lejeune M / Ivashchenko S / Bardiaux B / Vos M / Francetic O / Shevchik VE / Izadi-Pruneyre N / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Structure / Year: 2026
Title: Structural determinants of endopilus assembly, stability, and functional specificity in bacterial type II secretion.
Authors: Maylis Lejeune / Stefaniia Ivashchenko / Régine Dazzoni / Benjamin Bardiaux / Ravi R Sonani / Matthijn Vos / Theis Jacobsen / Edward H Egelman / Michael Nilges / Olivera Francetic / ...Authors: Maylis Lejeune / Stefaniia Ivashchenko / Régine Dazzoni / Benjamin Bardiaux / Ravi R Sonani / Matthijn Vos / Theis Jacobsen / Edward H Egelman / Michael Nilges / Olivera Francetic / Vladimir E Shevchik / Nadia Izadi-Pruneyre /
Abstract: Gram-negative bacteria employ the type II secretion system (T2SS) to transport folded protein effectors via a periplasmic helical polymer called the endopilus, composed of one major and four minor ...Gram-negative bacteria employ the type II secretion system (T2SS) to transport folded protein effectors via a periplasmic helical polymer called the endopilus, composed of one major and four minor pilin subunits. Endopili resemble type IV pili but feature a conserved calcium-binding site stabilizing their major pilins. Endopilus polymerization is coupled to substrate translocation through a dedicated outer membrane channel. We compared T2SSs from plant and human pathogens, Dickeya dadantii and Klebsiella oxytoca, respectively. Despite different ecological niches and secreted effectors, their major pilins (OutG and PulG) share >77% sequence identity. Using NMR and cryo-EM, we solved structures of calcium-bound OutG monomer, as well as OutG and PulG endopili at 3.6 Å resolution. Combining structural, mutational, and biophysical analyses with in vivo assays, we identified key determinants of secretion specificity and endopilus stability. Our findings reveal how minor sequence variations in conserved nanomachines drive functional adaptation to diverse environments.
History
DepositionMar 4, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75832.png

Downloads & links

-
Map

FileDownload / File: emd_75832.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 256 pix.
= 197.12 Å		0.77 Å/pix.
x 256 pix.
= 197.12 Å		0.77 Å/pix.
x 256 pix.
= 197.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.3268735 - 0.5721366
Average (Standard dev.)0.0018584507 (±0.025669977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 197.12 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_75832_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_75832_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_75832_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : OutG T2SS filament

EntireName: OutG T2SS filament
Components
  • Complex: OutG T2SS filament
    • Protein or peptide: Type II secretion system core protein G
  • Ligand: CALCIUM ION

-
Supramolecule #1: OutG T2SS filament

SupramoleculeName: OutG T2SS filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Dickeya dadantii (bacteria)

-
Macromolecule #1: Type II secretion system core protein G

MacromoleculeName: Type II secretion system core protein G / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Dickeya dadantii (bacteria)
Molecular weightTheoretical: 14.557503 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
FTLLEIMVVI VILGVLASLV VPNLMGNKEK ADRQKAISDI VALESALDMY KLDNSRYPTT EQGLGALVKK PTTPPEPRSY PQDGYIRRL PQDPWGAEYQ LVSPGRHGKV DVFSYGPDGM PDTDDDIGNW NVG

UniProtKB: Type II secretion system core protein G

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 10.775 Å
Applied symmetry - Helical parameters - Δ&Phi: 83.828 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1398406
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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