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- EMDB-46777: E. coli TolAQR conformation II -

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Basic information

Entry
Database: EMDB / ID: EMD-46777
TitleE. coli TolAQR conformation II
Map dataTolAQR conformation II
Sample
  • Complex: TolAQR complex conformation II
    • Protein or peptide: Tol-Pal system protein TolQ
    • Protein or peptide: Tol-Pal system protein TolA
    • Protein or peptide: Tol-Pal system protein TolR
KeywordsTol-Pal system / 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 division site / transmembrane transporter activity / disordered domain specific binding ...cellular response to bacteriocin / cell septum assembly / regulation of membrane invagination / bacteriocin transport / toxin transmembrane transporter activity / protein import / virion binding / 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
Tol-Pal system, TolQ / Tol-Pal system protein TolR / TolA C-terminal / 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 (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsCelia H / Botos I
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIA DK011011-17 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structures of the E. coli Ton and Tol motor complexes.
Authors: Herve Celia / Istvan Botos / Rodolfo Ghirlando / Denis Duché / Bridgette M Beach / Roland Lloubes / Susan K Buchanan /
Abstract: The Ton and Tol motor proteins use the proton gradient at the inner membrane of Gram-negative bacteria as an energy source. The generated force is transmitted through the periplasmic space to protein ...The Ton and Tol motor proteins use the proton gradient at the inner membrane of Gram-negative bacteria as an energy source. The generated force is transmitted through the periplasmic space to protein components associated with the outer membrane, either to maintain the outer membrane integrity for the Tol system, or to allow essential nutrients to enter the cell for Ton. We have solved the high-resolution structures of the E. coli TonB-ExbB-ExbD and TolA-TolQ-TolR complexes, revealing the inner membrane embedded engine parts of the Ton and Tol systems, and showing how TonB and TolA interact with the ExbBD and TolQR subcomplexes. Structural similarities between the two motor complexes suggest a common mechanism for the opening of the proton channel and the propagation of the proton motive force into movement of the TonB and TolA subunits. Because TonB and TolA bind at preferential ExbB or TolQ subunits, we propose a new mechanism of assembly of TonB and TolA with their respective ExbBD and TolQR subcomplexes and discuss its impact on the mechanism of action for the Ton and Tol systems.
History
DepositionAug 28, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46777.png

Downloads & links

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Map

FileDownload / File: emd_46777.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTolAQR conformation II
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.2653914 - 0.54608953
Average (Standard dev.)0.0005028952 (±0.020407487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap A

Fileemd_46777_half_map_1.map
Annotationhalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B

Fileemd_46777_half_map_2.map
Annotationhalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TolAQR complex conformation II

EntireName: TolAQR complex conformation II
Components
  • Complex: TolAQR complex conformation II
    • Protein or peptide: Tol-Pal system protein TolQ
    • Protein or peptide: Tol-Pal system protein TolA
    • Protein or peptide: Tol-Pal system protein TolR

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Supramolecule #1: TolAQR complex conformation II

SupramoleculeName: TolAQR complex conformation II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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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 (E. coli)
Molecular weightTheoretical: 25.623662 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 TolA

MacromoleculeName: Tol-Pal system protein TolA / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 44.563109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSWSHPQFE KGSSKATEQN DKLKRAIIIS AVLHVILFAA LIWSSFDENI EASAGGGGGS SIDAVMVDSG AVVEQYKRMQ SQESSAKRS DEQRKMKEQQ AAEELREKQA AEQERLKQLE KERLAAQEQK KQAEEAAKQA ELKQKQAEEA AAKAAADAKA K AEADAKAA ...String:
MGSWSHPQFE KGSSKATEQN DKLKRAIIIS AVLHVILFAA LIWSSFDENI EASAGGGGGS SIDAVMVDSG AVVEQYKRMQ SQESSAKRS DEQRKMKEQQ AAEELREKQA AEQERLKQLE KERLAAQEQK KQAEEAAKQA ELKQKQAEEA AAKAAADAKA K AEADAKAA EEAAKKAAAD AKKKAEAEAA KAAAEAQKKA EAAAAALKKK AEAAEAAAAE ARKKAATEAA EKAKAEAEKK AA AEKAAAD KKAAAEKAAA DKKAAEKAAA EKAAADKKAA AEKAAADKKA AAAKAAAEKA AAAKAAAEAD DIFGELSSGK NAP KTGGGA KGNNASPAGS GNTKNNGASG ADINNYAGQI KSAIESKFYD ASSYAGKTCT LRIKLAPDGM LLDIKPEGGD PALC QAALA AAKLAKIPKP PSQAVYEVFK NAPLDFKP

UniProtKB: Tol-Pal system protein TolA

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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 (E. coli)
Molecular weightTheoretical: 15.398884 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 61.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78674
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ddn:
E. coli TolAQR conformation II

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