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- EMDB-5901: 3D Reconstruction of Membrane Protein Complex ExbB4-ExbD2 -

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Basic information

Entry
Database: EMDB / ID: EMD-5901
Title3D Reconstruction of Membrane Protein Complex ExbB4-ExbD2
Map dataExbB4-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
KeywordsMembrane protein complex / coordinated rearrangement / flexible domain
Function / homology
Function and homology information


ferrichrome import into cell / energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / transmembrane transporter complex / plasma membrane protein complex / protein import / transmembrane transporter activity / membrane => GO:0016020 ...ferrichrome import into cell / energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / transmembrane transporter complex / plasma membrane protein complex / protein import / transmembrane transporter activity / membrane => GO:0016020 / cell outer membrane / protein transport / intracellular iron ion homeostasis / 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
Biopolymer transport protein ExbB / Biopolymer transport protein ExbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsSverzhinsky A / Fabre L / Cottreau AL / Biot-Pelletier DMP / Khalil S / Bostina M / Rouiller I / Coulton JW
CitationJournal: STRUCTURE / Year: 2014
Title: Coordinated Rearrangements between Cytoplasmic and Periplasmic Domains of the Membrane Protein Complex ExbB-ExbD of Escherichia coli
Authors: Sverzhinsky A / Fabre L / Cottreau AL / Biot-Pelletier DMP / Khalil S / Bostina M / Rouiller I / Coulton JW
History
DepositionFeb 12, 2014-
Header (metadata) releaseMar 5, 2014-
Map releaseApr 9, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.029
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_5901.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExbB4-ExbD2 complex with ExbD periplasmic domains unobservable
Voxel sizeX=Y=Z: 2.2 Å
Density
Contour LevelBy AUTHOR: 0.029 / Movie #1: 0.029
Minimum - Maximum-0.09642076 - 0.10619523
Average (Standard dev.)-0.00112127 (±0.01226369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0960.106-0.001

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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

EntireName: 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

SupramoleculeName: 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 weightTheoretical: 139 KDa

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Macromolecule #1: Biopolymer Transport Protein ExbB

MacromoleculeName: 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
Molecular weightTheoretical: 26 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: M15 / Recombinant plasmid: pQE60
SequenceUniProtKB: Biopolymer transport protein ExbB / GO: membrane => GO:0016020 / InterPro: TonB-system energizer ExbB type-1

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Macromolecule #2: Biopolymer Transport Protein ExbD

MacromoleculeName: Biopolymer Transport Protein ExbD / type: protein_or_peptide / ID: 2 / Name.synonym: ExbD / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12 / Location in cell: Cytoplasmic Membrane
Molecular weightTheoretical: 17 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: M15 / Recombinant plasmid: pQE60
SequenceUniProtKB: Biopolymer transport protein ExbD / GO: membrane => GO:0016020 / InterPro: TonB system transport protein ExbD type-1

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.5 / Details: 25 mM Tris-HCl, 150 mM NaCl, 0.01% DDM
StainingType: NEGATIVE
Details: Grids with adsorbed protein were stained with 1.5% uranyl formate for 1 minute.
GridDetails: 400 mesh copper grid with thin carbon support, glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 50,000x magnification
DateMar 27, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 67147 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 67000
Sample stageSpecimen holder: Room temperature / Specimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsManual particle picking from random conical tilt pairs, 3D classification, projection matching angular refinement
CTF correctionDetails: Each Micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: OTHER / Software - Name: Xmipp, EMAN2, SPARX / Number images used: 7322

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