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- EMDB-46779: E. coli TonB-ExbBD TonB bound to ExbB chain E -

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Basic information

Entry
Database: EMDB / ID: EMD-46779
TitleE. coli TonB-ExbBD TonB bound to ExbB chain E
Map dataTonB-ExbBD TonB bound to ExbB chainE
Sample
  • Complex: TonB-ExbBD complex
    • Protein or peptide: Biopolymer transport protein ExbB
    • Protein or peptide: Protein TonB
    • Protein or peptide: Biopolymer transport protein ExbD
KeywordsTon system / TRANSPORT PROTEIN
Function / homology
Function and homology information


receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / ferrichrome import into cell / energy transducer activity / bacteriocin transport / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / transmembrane transporter complex / plasma membrane protein complex ...receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / ferrichrome import into cell / energy transducer activity / bacteriocin transport / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / transmembrane transporter complex / plasma membrane protein complex / protein import / cell envelope / transmembrane transporter activity / cell outer membrane / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / protein stabilization / protein domain specific binding / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / TonB polyproline region / Gram-negative bacterial TonB protein / : / TonB C-terminal domain profile. / TonB-system energizer ExbB type-1 / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB system transport protein ExbD type-1 / TonB/TolA, C-terminal ...: / TonB polyproline region / Gram-negative bacterial TonB protein / : / TonB C-terminal domain profile. / TonB-system energizer ExbB type-1 / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB system transport protein ExbD type-1 / TonB/TolA, C-terminal / : / 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
Protein TonB / Biopolymer transport protein ExbB / Biopolymer transport protein ExbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 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_46779.png

Downloads & links

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Map

FileDownload / File: emd_46779.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTonB-ExbBD TonB bound to ExbB chainE
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: 0.085
Minimum - Maximum-0.22486754 - 0.48044428
Average (Standard dev.)-0.00043331445 (±0.01939409)
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_46779_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_46779_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 : TonB-ExbBD complex

EntireName: TonB-ExbBD complex
Components
  • Complex: TonB-ExbBD complex
    • Protein or peptide: Biopolymer transport protein ExbB
    • Protein or peptide: Protein TonB
    • Protein or peptide: Biopolymer transport protein ExbD

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Supramolecule #1: TonB-ExbBD complex

SupramoleculeName: TonB-ExbBD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: TonB bound to ExbB chainE
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Biopolymer transport protein ExbB

MacromoleculeName: Biopolymer transport protein ExbB / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.312322 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGNNLMQTDL SVWGMYQHAD IVVKCVMIGL ILASVVTWAI FFSKSVEFFN QKRRLKREQQ LLAEARSLNQ ANDIAADFGS KSLSLHLLN EAQNELELSE GSDDNEGIKE RTSFRLERRV AAVGRQMGRG NGYLATIGAI SPFVGLFGTV WGIMNSFIGI A QTQTTNLA ...String:
MGNNLMQTDL SVWGMYQHAD IVVKCVMIGL ILASVVTWAI FFSKSVEFFN QKRRLKREQQ LLAEARSLNQ ANDIAADFGS KSLSLHLLN EAQNELELSE GSDDNEGIKE RTSFRLERRV AAVGRQMGRG NGYLATIGAI SPFVGLFGTV WGIMNSFIGI A QTQTTNLA VVAPGIAEAL LATAIGLVAA IPAVVIYNVF ARQIGGFKAM LGDVAAQVLL LQSRDLDLEA SAAAHPVRVA QK LRAG

UniProtKB: Biopolymer transport protein ExbB

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Macromolecule #2: Protein TonB

MacromoleculeName: Protein TonB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 28.495709 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTLDLPRRFP WPTLLSVCIH GAVVAGLLYT SVHQVIELPA PAQPISVTMV TPADLEPPQA VQPPPEPVVE PEPEPEPIPE PPKEAPVVI EKPKPKPKPK PKPVKKVQEQ PKRDVKPVES RPASPFENTA PARLTSSTAT AATSKPVTSV ASGPRALSRN Q PQYPARAQ ...String:
MTLDLPRRFP WPTLLSVCIH GAVVAGLLYT SVHQVIELPA PAQPISVTMV TPADLEPPQA VQPPPEPVVE PEPEPEPIPE PPKEAPVVI EKPKPKPKPK PKPVKKVQEQ PKRDVKPVES RPASPFENTA PARLTSSTAT AATSKPVTSV ASGPRALSRN Q PQYPARAQ ALRIEGQVKV KFDVTPDGRV DNVQILSAKP ANMFEREVKN AMRRWRYEPG KPGSGIVVNI LFKINGTTEI QG GGSENLY FQGGSAWSHP QFEK

UniProtKB: Protein TonB

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Macromolecule #3: Biopolymer transport protein ExbD

MacromoleculeName: Biopolymer transport protein ExbD / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.161674 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAMHLNENLD DNGEMHDINV TPFIDVMLVL LIIFMVAAPL ATVDVKVNLP ASTSTPQPRP EKPVYLSVKA DNSMFIGNDP VTDETMITA LNALTEGKKD TTIFFRADKT VDYETLMKVM DTLHQAGYLK IGLVGEETAK AKENLYFQGN AGSGHHHHHH H HHH

UniProtKB: Biopolymer transport protein ExbD

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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 / Support film - Material: CARBON / Support film - topology: HOLEY
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: 69.9 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: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30556
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-9ddp:
E. coli TonB-ExbBD TonB bound to ExbB chain E

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