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3D Reconstruction of Membrane Protein Complex ExbB4-ExbD2

by single particle reconstruction, at 24 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.036, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.036, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5903
Title3D Reconstruction of Membrane Protein Complex ExbB4-ExbD2
MapExbB4-ExbD2 complex with ExbD periplasmic domains dimerized in the membrane-parallel position
SampleMembrane protein complex ExbB4-ExbD2 from Escherichia coli
KeywordsMembrane protein complex, coordinated rearrangement, flexible domain
AuthorsSverzhinsky A, Fabre L, Cottreau AL, Biot-Pelletier DMP, Khalil S, Bostina M, Rouiller I, Coulton JW
DateDeposition: 2014-02-12, Header release: 2014-03-05, Map release: 2014-04-09, Last update: 2016-02-17
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.036, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.036, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleStructure, Vol. 22, Issue 5, Page 791-797, Year 2014
TitleCoordinated rearrangements between cytoplasmic and periplasmic domains of the membrane protein complex ExbB-ExbD of Escherichia coli.
AuthorsAleksandr Sverzhinsky, Lucien Fabre, Andrew L Cottreau, Damien M P Biot-Pelletier, Sofia Khalil, Mihnea Bostina, Isabelle Rouiller, James W Coulton
Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B4, Canada.
Facility for Electron Microscope Research, McGill University, Montreal, QC H3A 2B4, Canada.
Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Microbiome and Disease Tolerance Centre, McGill University, Montreal, QC H3A 2B4, Canada.
KeywordsCell Membrane (metabolism), Cytoplasm (metabolism), Detergents (chemistry), Escherichia coli Proteins (chemistry), ExbB protein, E coli, Image Processing, Computer-Assisted (methods), Microscopy, Electron, Protein Structure, Tertiary, exbD protein, E coli (123424-75-9)
LinksPubMed: 24657092, PII: S0969-2126(14)00050-1, DOI: 10.1016/j.str.2014.02.010
Map
Fileemd_5903.map.gz ( map file in CCP4 format, 8193 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.2 A/pix
= 281.6 A
128 pix
2.2 A/pix
= 281.6 A
128 pix
2.2 A/pix
= 281.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.036 (by author), 0.036 (movie #1):
Minimum - Maximum: -0.08121978 - 0.09978295
Average (Standard dev.): -0.00111288 (0.01272697)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
Unit CellA= B= C: 281.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.2 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0810.100-0.001
Annotation DetailsExbB4-ExbD2 complex with ExbD periplasmic domains dimerized in the membrane-parallel position
Supplement
Sample
NameMembrane protein complex ExbB4-ExbD2 from Escherichia coli
Number of Components2
Oligomeric StateFour ExbB in complex with two ExbD
Theoretical Mass0.139MDa
Component #1: protein - ExbB
Scientific nameBiopolymer Transport Protein ExbB
Common NameExbB
Theoretical Mass0.026 MDa
Oligomeric DetailsTetramer
Number of Copies4
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
StrainK-12
Recombinant expressionYes
Natural SourceCell Location: Cytoplasmic Membrane
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Exp System Strain: M15
Vector: pQE60
LinksGene Ontology: GO:0016021, Uni Prot: P0ABU7, Inter Pro: IPR:014164
Component #2: protein - ExbD
Scientific nameBiopolymer Transport Protein ExbD
Common NameExbD
Theoretical Mass0.017 MDa
Oligomeric DetailsDimer
Number of Copies2
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
StrainK-12
Recombinant expressionYes
Natural SourceCell Location: Cytoplasmic Membrane
Engineered SourceVector: pQE60
NCBI taxonomy: 562
Expression system: Escherichia coli
Exp System Strain: M15
LinksInter Pro: IPR:014170, Uni Prot: P0ABV2, Gene Ontology: GO:0016021
Experiment
Sample Preparation
StainingGrids with adsorbed protein were stained with 1.5% uranyl formate for 1 minute.
Specimen Stateparticle
Specimen Conc0.02 mg/ml
Specimen Support Details400 mesh copper grid with thin carbon support, glow discharged
BufferDetails: 25 mM Tris-HCl, 150 mM NaCl, 0.01% DDM
pH: 7.5
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Date27-MAR-2013
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 67000, Calibrated: 67147
AstigmatismObjective lens astigmatism was corrected at 50,000x magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 3500 nm
Specimen Holder
HolderRoom temperature
ModelSIDE ENTRY, EUCENTRIC
Camera
DetectorGATAN ULTRASCAN 4000 (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmRandom conical tilt, ML3D classification
SoftwareXmipp, EMAN2, SPARX
CTF CorrectionEach Micrograph
Resolution By Author24 A
Resolution MethodFSC 0.5, semi-independent
Single Particle
Applied SymmetryC1 (asymmetric)
Number of Projections5562
DetailsManual particle picking from random conical tilt pairs, 3D classification, projection matching angular refinement
Download
Data from EMDB
Header (meta data in XML format)emd-5903.xml (9 KB)
Map dataemd_5903.map.gz (7.4 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5903
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 26.3 KB