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- EMDB-1356: Structural basis for the PufX-mediated dimerization of bacterial ... -

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Basic information

Entry
Database: EMDB / ID: 1356
TitleStructural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes.
SampleCore complex of Rhodobacter veldkampii
SourceRhodobacter veldkampii / archaea / ロドバクター・ヴェルドカンピイ
Map data3D map file of Rhobacter veldkampii LH1-RC obtained by cryoEM and low-pass filtered at a resolution of 11 angstroems
Methodsingle particle reconstruction, at 12 A resolution
AuthorsBusselez J / Cottevieille M / Cuniasse P / Boisset N / Levy D
CitationStructure, 2007, 15, 1674-1683

Structure, 2007, 15, 1674-1683 StrPapers
Structural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes.
Johan Busselez / Magali Cottevieille / Philippe Cuniasse / Francesca Gubellini / Nicolas Boisset / Daniel Lévy

DateDeposition: Apr 27, 2007 / Header (metadata) release: May 3, 2007 / Map release: Jan 7, 2008 / Last update: Apr 27, 2007

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0095
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0095
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1356.map.gz (map file in CCP4 format, 6099 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
116 pix
1.95 A/pix
= 226.2 A
116 pix
1.95 A/pix
= 226.2 A
116 pix
1.95 A/pix
= 226.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.95 A
Density
Contour Level:0.00493, 0.0095 (movie #1):
Minimum - Maximum-0.0353536 - 0.0627238
Average (Standard dev.)3.79676e-05 (0.00326315)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions116116116
Origin-58-58-58
Limit575757
Spacing116116116
CellA=B=C: 226.2 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.951.951.95
M x/y/z116116116
origin x/y/z0.0000.0000.000
length x/y/z226.200226.200226.200
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-58-58-58
NC/NR/NS116116116
D min/max/mean-0.0350.0630.000

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Supplemental data

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Sample components

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Entire Core complex of Rhodobacter veldkampii

EntireName: Core complex of Rhodobacter veldkampii / Oligomeric State: monomers / Number of components: 1
MassTheoretical: 300 kDa

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Component #1: protein, core complex of Rba. veldkampii

ProteinName: core complex of Rba. veldkampii / a.k.a: LH1-RC of Rba. veldkampii / Oligomeric Details: Monomer / Recombinant expression: No / Number of Copies: 1
MassExperimental: 300 kDa
SourceSpecies: Rhodobacter veldkampii / archaea / ロドバクター・ヴェルドカンピイ
Strain: DSM 11550

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1.5 mg/ml
Buffer solution: Glycine-glycine 50 mM, NaCl 200 mM, DOTM 0.1 %
pH: 7.6
StainingCRYOEM : 4 microL were applied on a Lacey Formwar grid.
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 93 K / Method: Manual single-sided blotting / Details: Vitrification instrument: manual plunger

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Electron microscopy imaging

ImagingMicroscope: JEOL 2010F / Date: Jun 1, 2005 / Details: low-dose illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 45000 X (nominal), 45000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1870 - 3460 nm
Specimen HolderHolder: Gatan / Model: GATAN LIQUID NITROGEN / Temperature: K ( 93 - 94 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 74 / Scanner: OTHER / Bit depth: 8 / Details: Scanner model : Nikon Coolscan 8000ED

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 27000
Details: Particles were semi-automatically selected using Boxer algorithm of EMAN software
Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: projection matching / Software: SPIDER / CTF correction: Wiener filtration on volumes / Resolution: 12 A / Resolution method: FSC 0.5
FSC plot (resolution assessment)

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