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- PDB-9ddo: E. coli TonB-ExbBD TonB bound to ExbB chain C -

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Basic information

Entry
Database: PDB / ID: 9ddo
TitleE. coli TonB-ExbBD TonB bound to ExbB chain C
Components
  • Biopolymer transport protein ExbB
  • Biopolymer transport protein ExbD
  • Protein TonB
KeywordsTRANSPORT PROTEIN / Ton system
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
Chem-PEV / Protein TonB / Biopolymer transport protein ExbB / Biopolymer transport protein ExbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsCelia, H. / Botos, I.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biopolymer transport protein ExbB
B: Biopolymer transport protein ExbB
C: Biopolymer transport protein ExbB
D: Biopolymer transport protein ExbB
E: Biopolymer transport protein ExbB
F: Protein TonB
Y: Biopolymer transport protein ExbD
Z: Biopolymer transport protein ExbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,82110
Polymers196,3818
Non-polymers1,4402
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Biopolymer transport protein ExbB


Mass: 26312.322 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: exbB, b3006, JW2974 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABU7
#2: Protein Protein TonB


Mass: 28495.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tonB, exbA, b1252, JW5195 / Production host: Escherichia coli (E. coli) / References: UniProt: P02929
#3: Protein Biopolymer transport protein ExbD


Mass: 18161.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: exbD, b3005, JW2973 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABV2
#4: Chemical ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 720.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: POPE, phospholipid*YM
Has ligand of interestY
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: TonB-ExbBD complex / Type: COMPLEX / Details: TonB bound to ExbB chainC / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 69.9 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5084: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227584 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049385
ELECTRON MICROSCOPYf_angle_d0.75312686
ELECTRON MICROSCOPYf_dihedral_angle_d4.9051345
ELECTRON MICROSCOPYf_chiral_restr0.0441496
ELECTRON MICROSCOPYf_plane_restr0.0031618

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