+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6927 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Ton system / ion channel / energizer / transporter / proton motive force / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
Authors | Yonekura K / Yamashita Y / Matsuoka R / Maki-Yonekura S | |||||||||
Funding support | Japan, 2 items
| |||||||||
Citation | Journal: Elife / Year: 2018 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6927.map.gz | 59.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6927-v30.xml emd-6927.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_6927.png | 66.9 KB | ||
Filedesc metadata | emd-6927.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6927 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6927 | HTTPS FTP |
-Validation report
Summary document | emd_6927_validation.pdf.gz | 463 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6927_full_validation.pdf.gz | 462.6 KB | Display | |
Data in XML | emd_6927_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_6927_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6927 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6927 | HTTPS FTP |
-Related structure data
Related structure data | 5zfuMC 6928C 5zfpC 5zfvC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_6927.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.2157 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)
Entire | Name: the ExbB/ExbD hexameric complex (ExbB6ExbD3TM) |
---|---|
Components |
|
-Supramolecule #1: the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)
Supramolecule | Name: the ExbB/ExbD hexameric complex (ExbB6ExbD3TM) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K-12 |
-Macromolecule #1: Biopolymer transport protein ExbB
Macromolecule | Name: Biopolymer transport protein ExbB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 |
Molecular weight | Theoretical: 26.312322 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: 22-mer peptide from Biopolymer transport protein ExbD
Macromolecule | Name: 22-mer peptide from Biopolymer transport protein ExbD / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 |
Molecular weight | Theoretical: 2.430062 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: NVTPFIDVML VLLIIFMVAA PL UniProtKB: Biopolymer transport protein ExbD |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL |
---|---|
Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.81195 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38323 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
---|---|
Output model | PDB-5zfu: |