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- EMDB-53394: cryo-EM structure of TolQRA in nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-53394
Titlecryo-EM structure of TolQRA in nanodiscs
Map data
Sample
  • Complex: cryo-EM structure of TolQRA in 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: 3.52 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

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Structure visualization

Supplemental images

emd_53394.png

Downloads & links

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Map

FileDownload / File: emd_53394.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0003
Minimum - Maximum-0.0063918876 - 1.7997923
Average (Standard dev.)0.001227453 (±0.027127123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53394_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_53394_half_map_2.map
Projections & Slices
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Sample components

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Entire : cryo-EM structure of TolQRA in nanodiscs

EntireName: cryo-EM structure of TolQRA in nanodiscs
Components
  • Complex: cryo-EM structure of TolQRA in 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

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Supramolecule #1: cryo-EM structure of TolQRA in nanodiscs

SupramoleculeName: cryo-EM structure of TolQRA in nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)

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Macromolecule #1: Tol-Pal system protein TolQ

MacromoleculeName: Tol-Pal system protein TolQ / type: protein_or_peptide / ID: 1 / 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

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Macromolecule #2: Tol-Pal system protein TolR

MacromoleculeName: Tol-Pal system protein TolR / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: Tol-Pal system protein TolA

MacromoleculeName: Tol-Pal system protein TolA / type: protein_or_peptide / ID: 3 / Number of copies: 3 / 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 57.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.74 µm / Nominal defocus min: 0.331 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181301
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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