+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6928 | |||||||||
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Title | Structure of the ExbB/ExbD pentameric complex (ExbB5ExbD1TM) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / protein import / plasma membrane protein complex / transmembrane transporter complex / transmembrane transporter activity / cell outer membrane / protein transport ...energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / protein import / plasma membrane protein complex / transmembrane transporter complex / transmembrane transporter activity / cell outer membrane / protein transport / intracellular iron ion homeostasis / protein stabilization / protein homodimerization activity / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Yonekura K / Yamashita Y / Matsuoka R / Maki-Yonekura S | |||||||||
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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6928.map.gz | 58.5 MB | EMDB map data format | |
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Header (meta data) | emd-6928-v30.xml emd-6928.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_6928.png | 104.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6928 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6928 | HTTPS FTP |
-Related structure data
Related structure data | 5zfvMC 6927C 5zfpC 5zfuC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6928.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.056 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : the ExbB/ExbD pentameric complex (ExbB5ExbD1TM)
Entire | Name: the ExbB/ExbD pentameric complex (ExbB5ExbD1TM) |
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Components |
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-Supramolecule #1: the ExbB/ExbD pentameric complex (ExbB5ExbD1TM)
Supramolecule | Name: the ExbB/ExbD pentameric complex (ExbB5ExbD1TM) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K12 |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Biopolymer transport protein ExbB
Macromolecule | Name: Biopolymer transport protein ExbB / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
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 |
-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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 2.430062 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: NVTPFIDVML VLLIIFMVAA PL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5.4 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.3 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: PROJECTION MATCHING |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22243 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-5zfv: |