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Open data
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Basic information
Entry | Database: PDB / ID: 5zfu | |||||||||
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Title | Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM) | |||||||||
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![]() | TRANSPORT PROTEIN / Ton system / ion channel / energizer / transporter / proton motive force | |||||||||
Function / homology | ![]() energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / protein import / transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / protein transport ...energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / protein import / transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / protein transport / intracellular iron ion homeostasis / protein stabilization / protein homodimerization activity / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
![]() | Yonekura, K. / Yamashita, Y. / Matsuoka, R. / Maki-Yonekura, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Hexameric and pentameric complexes of the ExbBD energizer in the Ton system. Authors: Saori Maki-Yonekura / Rei Matsuoka / Yoshiki Yamashita / Hirofumi Shimizu / Maiko Tanaka / Fumie Iwabuki / Koji Yonekura / ![]() Abstract: Gram-negative bacteria import essential nutrients such as iron and vitamin B through outer membrane receptors. This process utilizes proton motive force harvested by the Ton system made up of three ...Gram-negative bacteria import essential nutrients such as iron and vitamin B through outer membrane receptors. This process utilizes proton motive force harvested by the Ton system made up of three inner membrane proteins, ExbB, ExbD and TonB. ExbB and ExbD form the proton channel that energizes uptake through TonB. Recently, crystal structures suggest that the ExbB pentamer is the scaffold. Here, we present structures of hexameric complexes of ExbB and ExbD revealed by X-ray crystallography and single particle cryo-EM. Image analysis shows that hexameric and pentameric complexes coexist, with the proportion of hexamer increasing with pH. Channel current measurement and 2D crystallography support the existence and transition of the two oligomeric states in membranes. The hexameric complex consists of six ExbB subunits and three ExbD transmembrane helices enclosed within the central channel. We propose models for activation/inactivation associated with hexamer and pentamer formation and utilization of proton motive force. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.9 KB | Display | ![]() |
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PDB format | ![]() | 177.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6927MC ![]() 6928C ![]() 5zfpC ![]() 5zfvC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 26312.322 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 2430.062 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: the ExbB/ExbD hexameric complex (ExbB6ExbD3TM) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 0.81195 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38323 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |