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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, Image by UCSF CHIMERA

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

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

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

Density
Contour Level:0.00493, 0.0095 (movie #1):
Minimum - Maximum: -0.0353536 - 0.0627238
Average (Standard dev.): 3.79676e-05 (0.00326315)
Data TypeImage stored as Reals
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
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 SO-163 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 0.5
Single Particle
Number of Projections27000
DetailsParticles were semi-automatically selected using Boxer algorithm of EMAN software
Applied SymmetryC1 (asymmetric)
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