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Structural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes.

by single particle reconstruction, at 12 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0095, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0095, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1356
TitleStructural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes.
Map3D map file of Rhobacter veldkampii LH1-RC obtained by cryoEM and low-pass filtered at a resolution of 11 angstroems
SampleCore complex of Rhodobacter veldkampii
AuthorsBusselez J, Cottevieille M, Cuniasse P, Boisset N, Levy D
DateDeposition: 2007-04-27, Header release: 2007-05-03, Map release: 2008-01-07, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0095, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0095, Made by UCSF CHIMERA

Supplemental images

EMD-1356.png

FSC_graph_em...
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

PDB-1mhs

EMDB-2334

EMDB-1711

PDB-4au6
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleStructure, Vol. 15, Issue 12, Page 1674-83, Year 2007
TitleStructural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes.
AuthorsJohan Busselez, Magali Cottevieille, Philippe Cuniasse, Francesca Gubellini, Nicolas Boisset, Daniel Lévy
Institut Curie, UMR-CNRS 168, 11 rue Pierre et Marie Curie, F-75231 Paris Cedex 05, France.
KeywordsAmino Acid Sequence, Bacterial Proteins (chemistry), Cryoelectron Microscopy, Dimerization, Models, Molecular, Molecular Sequence Data, Photosynthesis, Protein Conformation, Rhodobacter sphaeroides (chemistry), Sequence Homology, Amino Acid
LinksPII: S0969-2126(07)00418-2, DOI: 10.1016/j.str.2007.09.026, PubMed: 18073116
Map
FileEMD-1356.map ( map file in CCP4 format, 6244 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.00493, 0.0095 (movie #1):
Minimum - Maximum: -0.0353536 - 0.0627238
Average (Standard dev.): 3.79676e-05 (0.00326315)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions116116116
Origin-58-58-58
Limit575757
Spacing116116116
Unit CellA= B= C: 226.2 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.95 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0350.0630.000
Annotation Details3D map file of Rhobacter veldkampii LH1-RC obtained by cryoEM and low-pass filtered at a resolution of 11 angstroems
Supplement
Images
Images

EMD-1356.png
FSC
FSC
Others
ImageFile: FSC_graph_emd_1356.tif
Sample
NameCore complex of Rhodobacter veldkampii
Oligomeric Statemonomers
Number of Components1
Theoretical Mass0.3MDa
Component #1: protein - LH1-RC of Rba. veldkampii
Scientific namecore complex of Rba. veldkampii
Common NameLH1-RC of Rba. veldkampii
Experimental Mass0.3 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesRhodobacter veldkampii
NCBI taxonomy33049
StrainDSM 11550
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Conc1.5 mg/ml
StainingCRYOEM : 4 microL were applied on a Lacey Formwar grid.
Specimen Stateparticle
BufferDetails: Glycine-glycine 50 mM, NaCl 200 mM, DOTM 0.1 %
pH: 7.6
Vitrification
Cryogen NameETHANE
Temperature93 Kelvin
InstrumentHOMEMADE PLUNGER
MethodManual single-sided blotting
DetailsVitrification instrument: manual plunger
Imaging
MicroscopeJEOL 2010F
Date2005-06-01
Detailslow-dose illumination
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 45000, Calibrated: 45000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1870 nm - 3460 nm
Specimen Holder
HolderGatan
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature K ( 93 - 94 K)
Camera
DetectorKodak SO163 film
Image Acquisition
Number of Digital Images74
Quant Bit Number8
ScannerOTHER
DetailsScanner model : Nikon Coolscan 8000ED
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmprojection matching
SoftwareSPIDER
CTF CorrectionWiener filtration on volumes
Resolution By Author
12 A
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections27000
DetailsParticles were semi-automatically selected using Boxer algorithm of EMAN software
Download
Data from EMDB
Header (meta data in XML format)emd-1356.xml (7.6 KB)
Map dataemd_1356.map.gz (5.6 MB)
ImagesEMD-1356.png (148.4 KB)
FSC (resolution estimation)emd_1356_fsc.xml (4.3 KB)
OthersFSC_graph_emd_1356.tif (145.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1356
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 19.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 20 KB