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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: Celia, H. / Botos, I. / Ghirlando, R. / Duche, D. / Beach, B.M. / Lloubes, R. / Buchanan, S.K.
History
DepositionAug 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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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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