- EMDB-5901: 3D Reconstruction of Membrane Protein Complex ExbB4-ExbD2 -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-5901
Title
3D Reconstruction of Membrane Protein Complex ExbB4-ExbD2
Map data
ExbB4-ExbD2 complex with ExbD periplasmic domains unobservable
Sample
Sample: Membrane protein complex ExbB4-ExbD2 from Escherichia coli
Protein or peptide: Biopolymer Transport Protein ExbB
Protein or peptide: Biopolymer Transport Protein ExbD
Keywords
Membrane protein complex / coordinated rearrangement / flexible domain
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 / membrane => GO:0016020 / protein stabilization / protein homodimerization activity / identical protein binding / membrane / plasma membrane Similarity search - Function
TonB-system energizer ExbB type-1 / TonB-system energizer ExbB type-1 / TonB system transport protein ExbD type-1 / TonB system transport protein ExbD type-1 / 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
Journal: Structure / Year: 2014 Title: Coordinated rearrangements between cytoplasmic and periplasmic domains of the membrane protein complex ExbB-ExbD of Escherichia coli. Authors: Aleksandr Sverzhinsky / Lucien Fabre / Andrew L Cottreau / Damien M P Biot-Pelletier / Sofia Khalil / Mihnea Bostina / Isabelle Rouiller / James W Coulton / Abstract: Gram-negative bacteria rely on the ExbB-ExbD-TonB system for the import of essential nutrients. Despite decades of research, the stoichiometry, subunit organization, and mechanism of action of the ...Gram-negative bacteria rely on the ExbB-ExbD-TonB system for the import of essential nutrients. Despite decades of research, the stoichiometry, subunit organization, and mechanism of action of the membrane proteins of the Ton system remain unclear. We copurified ExbB with ExbD as an ∼240 kDa protein-detergent complex, measured by light scattering and by native gels. Quantitative Coomassie staining revealed a stoichiometry of ExbB4-ExbD2. Negative stain electron microscopy and 2D analysis showed particles of ∼10 nm diameter in multiple structural states. Nanogold labeling identified the position of the ExbD periplasmic domain. Random conical tilt was used to reconstruct the particles in three structural states followed by sorting of the single particles and refinement of each state. The different states are interpreted by coordinated structural rearrangements between the cytoplasmic domain and the periplasmic domain, concordant with in vivo predictions.
History
Deposition
Feb 12, 2014
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Header (metadata) release
Mar 5, 2014
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Map release
Apr 9, 2014
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Update
Feb 17, 2016
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Current status
Feb 17, 2016
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_5901.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
ExbB4-ExbD2 complex with ExbD periplasmic domains unobservable
Voxel size
X=Y=Z: 2.2 Å
Density
Contour Level
By AUTHOR: 0.029 / Movie #1: 0.029
Minimum - Maximum
-0.09642076 - 0.10619523
Average (Standard dev.)
-0.00112127 (±0.01226369)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
128
128
128
Spacing
128
128
128
Cell
A=B=C: 281.6 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.2
2.2
2.2
M x/y/z
128
128
128
origin x/y/z
0.000
0.000
0.000
length x/y/z
281.600
281.600
281.600
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
128
128
128
D min/max/mean
-0.096
0.106
-0.001
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Supplemental data
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Sample components
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Entire : Membrane protein complex ExbB4-ExbD2 from Escherichia coli
Entire
Name: Membrane protein complex ExbB4-ExbD2 from Escherichia coli
Components
Sample: Membrane protein complex ExbB4-ExbD2 from Escherichia coli
Protein or peptide: Biopolymer Transport Protein ExbB
Protein or peptide: Biopolymer Transport Protein ExbD
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Supramolecule #1000: Membrane protein complex ExbB4-ExbD2 from Escherichia coli
Supramolecule
Name: Membrane protein complex ExbB4-ExbD2 from Escherichia coli type: sample / ID: 1000 / Oligomeric state: Four ExbB in complex with two ExbD / Number unique components: 2
Molecular weight
Theoretical: 139 KDa
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Macromolecule #1: Biopolymer Transport Protein ExbB
Macromolecule
Name: Biopolymer Transport Protein ExbB / type: protein_or_peptide / ID: 1 / Name.synonym: ExbB / Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: Yes
Source (natural)
Organism: Escherichia coli (E. coli) / Strain: K-12 / Location in cell: Cytoplasmic Membrane
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