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- PDB-9qvd: cryo-EM structure of TolQRA in nanodiscs -

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Basic information

Entry
Database: PDB / ID: 9qvd
Titlecryo-EM structure of TolQRA in nanodiscs
Components
  • Tol-Pal system protein TolA
  • Tol-Pal system protein TolQ
  • Tol-Pal system protein TolR
KeywordsMEMBRANE PROTEIN / Molecular motor Multi-pass membrane protein Accumulates at cell constriction sites.
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsLuo, Y. / Shen, C.
Funding support China, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tol-Pal system protein TolQ
B: Tol-Pal system protein TolQ
C: Tol-Pal system protein TolQ
D: Tol-Pal system protein TolQ
E: Tol-Pal system protein TolQ
F: Tol-Pal system protein TolR
G: Tol-Pal system protein TolR
H: Tol-Pal system protein TolA
I: Tol-Pal system protein TolA
J: Tol-Pal system protein TolA


Theoretical massNumber of molelcules
Total (without water)288,61410
Polymers288,61410
Non-polymers00
Water00
1


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

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Components

#1: Protein
Tol-Pal system protein TolQ


Mass: 25623.662 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: tolQ, fii, b0737, JW0727 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABU9
#2: Protein Tol-Pal system protein TolR


Mass: 15398.884 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: tolR, b0738, JW0728 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABV6
#3: Protein Tol-Pal system protein TolA


Mass: 43232.699 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: tolA, cim, excC, lky, b0739, JW0729 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19934
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: cryo-EM structure of TolQRA in nanodiscs / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2740 nm / Nominal defocus min: 331 nm
Image recordingElectron dose: 57.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181301 / Symmetry type: POINT
RefinementHighest resolution: 3.52 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029751
ELECTRON MICROSCOPYf_angle_d0.41213193
ELECTRON MICROSCOPYf_dihedral_angle_d3.2941303
ELECTRON MICROSCOPYf_chiral_restr0.0351536
ELECTRON MICROSCOPYf_plane_restr0.0031664

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