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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: EMD-1356
TitleStructural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes.
Map data3D map file of Rhobacter veldkampii LH1-RC obtained by cryoEM and low-pass filtered at a resolution of 11 angstroems
Sample
  • Sample: Core complex of Rhodobacter veldkampii
  • Protein or peptide: core complex of Rba. veldkampii
Biological speciesRhodobacter veldkampii (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 12.0 Å
AuthorsBusselez J / Cottevieille M / Cuniasse P / Boisset N / Levy D
CitationJournal: Structure / Year: 2007
Title: Structural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes.
Authors: Johan Busselez / Magali Cottevieille / Philippe Cuniasse / Francesca Gubellini / Nicolas Boisset / Daniel Lévy /
Abstract: In Rhodobacter (Rba.) sphaeroides, the subunit PufX is involved in the dimeric organization of the core complex. Here, we report the 3D reconstruction at 12 A by cryoelectron microscopy of the core ...In Rhodobacter (Rba.) sphaeroides, the subunit PufX is involved in the dimeric organization of the core complex. Here, we report the 3D reconstruction at 12 A by cryoelectron microscopy of the core complex of Rba. veldkampii, a complex of approximately 300 kDa without symmetry. The core complex is monomeric and constituted by a light-harvesting complex 1 (LH1) ring surrounding a uniquely oriented reaction center (RC). The LH1 consists of 15 resolved alpha/beta heterodimers and is interrupted. Within the opening, PufX polypeptide is assigned at a position facing the Q(B) site of the RC. This core complex is different from a dissociated dimer of the core complex of Rba. sphaeroides revealing that PufX in Rba. veldkampii is unable to dimerize. The absence in PufX of Rba. veldkampii of a G(31)XXXG(35) dimerization motif highlights the transmembrane interactions between PufX subunits involved in the dimerization of the core complexes of Rhodobacter species.
History
DepositionApr 27, 2007-
Header (metadata) releaseMay 3, 2007-
Map releaseJan 7, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1356.png

emd_1356.tif

Downloads & links

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Map

FileDownload / File: emd_1356.map.gz / Format: CCP4 / Size: 5.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map file of Rhobacter veldkampii LH1-RC obtained by cryoEM and low-pass filtered at a resolution of 11 angstroems
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.95 Å/pix.
x 116 pix.
= 226.2 Å		1.95 Å/pix.
x 116 pix.
= 226.2 Å		1.95 Å/pix.
x 116 pix.
= 226.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.95 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00493 / Movie #1: 0.0095
Minimum - Maximum-0.0353536 - 0.0627238
Average (Standard dev.)0.0000379676 (±0.00326315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-58-58-58
Dimensions116116116
Spacing116116116
CellA=B=C: 226.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
Components
  • Sample: Core complex of Rhodobacter veldkampii
  • Protein or peptide: core complex of Rba. veldkampii

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Supramolecule #1000: Core complex of Rhodobacter veldkampii

SupramoleculeName: Core complex of Rhodobacter veldkampii / type: sample / ID: 1000 / Oligomeric state: monomers / Number unique components: 1
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: core complex of Rba. veldkampii

MacromoleculeName: core complex of Rba. veldkampii / type: protein_or_peptide / ID: 1 / Name.synonym: LH1-RC of Rba. veldkampii / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Rhodobacter veldkampii (bacteria) / Strain: DSM 11550
Molecular weightExperimental: 300 KDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.6 / Details: Glycine-glycine 50 mM, NaCl 200 mM, DOTM 0.1 %
StainingType: NEGATIVE
Details: CRYOEM : 4 microL were applied on a Lacey Formwar grid.
VitrificationCryogen name: ETHANE / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger / Method: Manual single-sided blotting

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 93 K / Max: 94 K
Detailslow-dose illumination
DateJun 1, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Number real images: 74 / Average electron dose: 10 e/Å2 / Details: Scanner model : Nikon Coolscan 8000ED / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 45000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.46 µm / Nominal defocus min: 1.87 µm / Nominal magnification: 45000
Sample stageSpecimen holder: Gatan / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsParticles were semi-automatically selected using Boxer algorithm of EMAN software
CTF correctionDetails: Wiener filtration on volumes
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 27000
FSC plot (resolution estimation)

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