[English] 日本語
Yorodumi
- EMDB-53380: cryo-EM structure of TolQR conformation2 in SMA nanodiscs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53380
Titlecryo-EM structure of TolQR conformation2 in SMA nanodiscs
Map data
Sample
  • Complex: cryo-EM structure of TolQR conformation2 in SMA nanodiscs
    • Protein or peptide: Tol-Pal system protein TolQ
    • Protein or peptide: Tol-Pal system protein TolR
    • Protein or peptide: Tol-Pal system protein TolA
KeywordsMolecular motor Multi-pass membrane protein Accumulates at cell constriction sites. / MEMBRANE PROTEIN
Function / homology
Function and homology information


cellular response to bacteriocin / cell septum assembly / regulation of membrane invagination / bacteriocin transport / toxin transmembrane transporter activity / protein import / virion binding / cell envelope / cell division site / transmembrane transporter activity ...cellular response to bacteriocin / cell septum assembly / regulation of membrane invagination / bacteriocin transport / toxin transmembrane transporter activity / protein import / virion binding / cell envelope / cell division site / transmembrane transporter activity / disordered domain specific binding / protein transport / protein domain specific binding / cell division / symbiont entry into host cell / membrane / plasma membrane
Similarity search - Function
TolA C-terminal / Tol-Pal system, TolQ / Tol-Pal system protein TolR / Tol-Pal system, TolA / : / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family
Similarity search - Domain/homology
Tol-Pal system protein TolQ / Tol-Pal system protein TolR / Tol-Pal system protein TolA
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsLuo Y / Shen C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170029 China
CitationJournal: Cell Discov / Year: 2025
Title: Deciphering the molecular mechanism of the bacterial division motor TolQRA.
Authors: Chongrong Shen / Teng Xie / Yongbo Luo / Fangyuan Zhao / Xin Wang / Zhibo Zhang / Jie Pang / Jierou Zhang / Xintan Dong / Shenghai Chang / Bi-Sen Ding / Binwu Ying / Wei Chi / Zhaoming Su / ...Authors: Chongrong Shen / Teng Xie / Yongbo Luo / Fangyuan Zhao / Xin Wang / Zhibo Zhang / Jie Pang / Jierou Zhang / Xintan Dong / Shenghai Chang / Bi-Sen Ding / Binwu Ying / Wei Chi / Zhaoming Su / Ruhong Zhou / Xiaodi Tang / Haohao Dong /
Abstract: The Tol-Pal system is essential for maintaining outer membrane (OM) stability during cell division in Gram-negative bacteria. The inner membrane complex TolQRA harnesses proton motive force (PMF) to ...The Tol-Pal system is essential for maintaining outer membrane (OM) stability during cell division in Gram-negative bacteria. The inner membrane complex TolQRA harnesses proton motive force (PMF) to establish transient interactions within the periplasm, thereby coordinating cell envelope remodeling and facilitating OM invagination at division sites. However, the precise mechanism remains unclear. Here, we present cryo-electron microscopy structures of Escherichia coli TolQRA in multiple conformational states at 2.92-3.52 Å resolution, revealing rotary dynamics within the complex. Computational simulations reveal a proton-conductive channel comprising the putative proton-accepting residue Asp23 and the conserved polar residues Thr145 and Thr178, with monitored inter-residue distances providing support for a proton-driven rotary mechanism. Site-directed mutagenesis combined with functional assays validates the AlphaFold-predicted structure of the periplasmic domains of TolR and TolA, and further pinpoints critical residues required for complex function. Together, these findings advance our understanding of TolQRA-mediated proton transduction and offer new avenues for antibiotic drug development.
History
DepositionApr 11, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53380.png

Downloads & links

-
Map

FileDownload / File: emd_53380.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.)
1.1 Å/pix.
x 224 pix.
= 246.4 Å		1.1 Å/pix.
x 224 pix.
= 246.4 Å		1.1 Å/pix.
x 224 pix.
= 246.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0291
Minimum - Maximum-0.0016250806 - 1.9200342
Average (Standard dev.)0.0015072178 (±0.029012233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 246.40001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_53380_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_53380_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : cryo-EM structure of TolQR conformation2 in SMA nanodiscs

EntireName: cryo-EM structure of TolQR conformation2 in SMA nanodiscs
Components
  • Complex: cryo-EM structure of TolQR conformation2 in SMA nanodiscs
    • Protein or peptide: Tol-Pal system protein TolQ
    • Protein or peptide: Tol-Pal system protein TolR
    • Protein or peptide: Tol-Pal system protein TolA

-
Supramolecule #1: cryo-EM structure of TolQR conformation2 in SMA nanodiscs

SupramoleculeName: cryo-EM structure of TolQR conformation2 in SMA nanodiscs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)

-
Macromolecule #1: Tol-Pal system protein TolA

MacromoleculeName: Tol-Pal system protein TolA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Molecular weightTheoretical: 43.232699 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSKATEQNDK LKRAIIISAV LHVILFAALI WSSFDENIEA SAGGGGGSSI DAVMVDSGAV VEQYKRMQSQ ESSAKRSDEQ RKMKEQQAA EELREKQAAE QERLKQLEKE RLAAQEQKKQ AEEAAKQAEL KQKQAEEAAA KAAADAKAKA EADAKAAEEA A KKAAADAK ...String:
MSKATEQNDK LKRAIIISAV LHVILFAALI WSSFDENIEA SAGGGGGSSI DAVMVDSGAV VEQYKRMQSQ ESSAKRSDEQ RKMKEQQAA EELREKQAAE QERLKQLEKE RLAAQEQKKQ AEEAAKQAEL KQKQAEEAAA KAAADAKAKA EADAKAAEEA A KKAAADAK KKAEAEAAKA AAEAQKKAEA AAAALKKKAE AAEAAAAEAR KKAATEAAEK AKAEAEKKAA AEKAAADKKA AA EKAAADK KAAEKAAAEK AAADKKAAAE KAAADKKAAA AKAAAEKAAA AKAAAEADDI FGELSSGKNA PKTGGGAKGN NAS PAGSGN TKNNGASGAD INNYAGQIKS AIESKFYDAS SYAGKTCTLR IKLAPDGMLL DIKPEGGDPA LCQAALAAAK LAKI PKPPS QAVYEVFKNA PLDFKP

UniProtKB: Tol-Pal system protein TolA

-
Macromolecule #2: Tol-Pal system protein TolQ

MacromoleculeName: Tol-Pal system protein TolQ / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Molecular weightTheoretical: 25.623662 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTDMNILDLF LKASLLVKLI MLILIGFSIA SWAIIIQRTR ILNAAAREAE AFEDKFWSGI ELSRLYQESQ GKRDNLTGSE QIFYSGFKE FVRLHRANSH APEAVVEGAS RAMRISMNRE LENLETHIPF LGTVGSISPY IGLFGTVWGI MHAFIALGAV K QATLQMVA ...String:
MTDMNILDLF LKASLLVKLI MLILIGFSIA SWAIIIQRTR ILNAAAREAE AFEDKFWSGI ELSRLYQESQ GKRDNLTGSE QIFYSGFKE FVRLHRANSH APEAVVEGAS RAMRISMNRE LENLETHIPF LGTVGSISPY IGLFGTVWGI MHAFIALGAV K QATLQMVA PGIAEALIAT AIGLFAAIPA VMAYNRLNQR VNKLELNYDN FMEEFTAILH RQAFTVSESN KG

UniProtKB: Tol-Pal system protein TolQ

-
Macromolecule #3: Tol-Pal system protein TolR

MacromoleculeName: Tol-Pal system protein TolR / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Molecular weightTheoretical: 15.398884 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARARGRGRR DLKSEINIVP LLDVLLVLLL IFMATAPIIT QSVEVDLPDA TESQAVSSND NPPVIVEVSG IGQYTVVVEK DRLERLPPE QVVAEVSSRF KANPKTVFLI GGAKDVPYDE IIKALNLLHS AGVKSVGLMT QPI

UniProtKB: Tol-Pal system protein TolR

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.555 µm / Nominal defocus min: 0.647 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 228227
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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