[English] 日本語
Yorodumi
- EMDB-72687: Tetrameric InvE from Salmonella Typhimurium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72687
TitleTetrameric InvE from Salmonella Typhimurium
Map data
Sample
  • Complex: InvE
    • Protein or peptide: Invasion protein InvE
Keywordstetramer / gatekeeper protein / T3SS / PROTEIN TRANSPORT
Function / homology
Function and homology information


protein secretion by the type III secretion system / outer membrane / negative regulation of protein secretion / cell surface / plasma membrane
Similarity search - Function
Salmonella/Shigella invasion protein E / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain
Similarity search - Domain/homology
Invasion protein InvE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsZhu LY / Wang TT / Guo EZ / Lara-Tejero M / Galan JE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI030492 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Oligomeric assembly of the gatekeeper InvE orchestrates hierarchical type III protein secretion in Typhimurium.
Authors: Tingting Wang / Liyan Zhu / Emily Guo / Chunxiang Wu / Florian Schueder / Maria Lara-Tejero / Jorge E Galán /
Abstract: Type III secretion systems (T3SS) are critical virulence machines in many Gram-negative bacteria, enabling hierarchical secretion of translocases followed by effectors. In the serovar Typhimurium ...Type III secretion systems (T3SS) are critical virulence machines in many Gram-negative bacteria, enabling hierarchical secretion of translocases followed by effectors. In the serovar Typhimurium SPI-1 T3SS, the regulatory protein InvE (SctW) enforces this order. Here, we show that InvE assembles into tetramers and higher-order oligomers and that oligomerization is essential for function. A 2.4 Å cryo-electron microscopy (cryo-EM) structure reveals a tetramer built as a dimer of antiparallel dimers. Photocrosslinking maps one set of residues to the interdimer seams in this tetramer, while crosslinks from additional sites suggest lateral docking between dimers in alternative registries in vivo. Blue-native electrophoresis and SEC-MALS detect native high-molecular-weight species consistent with such assemblies. DNA-PAINT superresolution microscopy confirms the presence of higher-order InvE oligomers in vivo. Charge-reversal mutations that disrupt oligomerization collapse InvE to monomers and abolish secretion, effector translocation, invasion, and virulence. Together, these data define an oligomerization-based switch in which InvE reuses the dimeric face to form higher-order contacts that govern the transition from translocase to effector secretion.
History
DepositionSep 13, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72687.png

Downloads & links

-
Map

FileDownload / File: emd_72687.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 224 pix.
= 186.368 Å		0.83 Å/pix.
x 224 pix.
= 186.368 Å		0.83 Å/pix.
x 224 pix.
= 186.368 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.10803829 - 0.2634419
Average (Standard dev.)0.00018931099 (±0.008824524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 186.36801 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_72687_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_72687_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_72687_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_72687_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : InvE

EntireName: InvE
Components
  • Complex: InvE
    • Protein or peptide: Invasion protein InvE

-
Supramolecule #1: InvE

SupramoleculeName: InvE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: In Salmonella enterica serovar Typhimurium, the SPI 1 gatekeeper InvE governs the hierarchical secretion of T3SS substrates. Here InvE forms a homotetramer. Its oligomeric assemblies is essential for function.
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

-
Macromolecule #1: Invasion protein InvE

MacromoleculeName: Invasion protein InvE / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 45.538781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM IPGSTSGISF SRILSRQTSH QDATQHTDAQ QAEIQQAAED SSPGAEVQKF VQSTDEMSA ALAQFRNRRD YEKKSSNLSN SFERVLEDEA LPKAKQILKL ISVHGGALED FLRQARSLFP DPSDLVLVLR E LLRRKDLE ...String:
MGSSHHHHHH SSGLVPRGSH MASMTGGQQM IPGSTSGISF SRILSRQTSH QDATQHTDAQ QAEIQQAAED SSPGAEVQKF VQSTDEMSA ALAQFRNRRD YEKKSSNLSN SFERVLEDEA LPKAKQILKL ISVHGGALED FLRQARSLFP DPSDLVLVLR E LLRRKDLE EIVRKKLESL LKHVEEQTDP KTLKAGINCA LKARLFGKTL SLKPGLLRAS YRQFIQSESH EVEIYSDWIA SY GYQRRLV VLDFIEGSLL TDIDANDASC SRLEFGQLLR RLTQLKMLRS ADLLFVSTLL SYSFTKAFNA EESSWLLLML SLL QQPHEV DSLLADIIGL NALLLSHKEH ASFLQIFYQV CKAIPSSLFY EEYWQEELLM ALRSMTDIAY KHEMAEQRRT IEKL S

UniProtKB: Invasion protein InvE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: alphafold prediected model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1)
Software - details: local refinement job was used to generate the final map
Number images used: 2169983
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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