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Ribosome structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)

by single particle reconstruction, at 24 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.623970818, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 1.623970818, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5041
TitleRibosome structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)
MapRibosome structure from Desulfovibrio vulgaris Hildenborough (DvH)
Sample70S ribosome from Desulfovibrio vulgaris Hildenborough
KeywordsRibosome, Desulfovibrio vulgaris, DvH
AuthorsHan B-G, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowska HE, Ball DA, Typke D, Downing KH, Shatsky M, Brenner SE, Chandonia J-M, Biggin MD, Glaeser RM
DateDeposition: 2009-01-08, Header release: 2009-01-21, Map release: 2009-09-04, Last update: 2011-09-23
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.623970818, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 1.623970818, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Cite: data citing same article

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Diagram

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EMDB-1005
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 106, Issue 39, Page 16580-5, Year 2009
TitleSurvey of large protein complexes in D. vulgaris reveals great structural diversity.
AuthorsBong-Gyoon Han, Ming Dong, Haichuan Liu, Lauren Camp, Jil Geller, Mary Singer, Terry C Hazen, Megan Choi, H Ewa Witkowska, David A Ball, Dieter Typke, Kenneth H Downing, Maxim Shatsky, Steven E Brenner, John-Marc Chandonia, Mark D Biggin, Robert M Glaeser
Life Sciences, Genomics, Earth Sciences, and Physical Biosciences Divisions, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
KeywordsBacterial Proteins (chemistry), Crystallography, X-Ray, Databases, Protein, Desulfovibrio vulgaris (chemistry), Models, Molecular, Multiprotein Complexes (chemistry), Protein Conformation
LinksDOI: 10.1073/pnas.0813068106, PubMed: 19805340, PMC: PMC2742403
Map
FileEMD-5041.map ( map file in CCP4 format, 8390 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:1.48 (by author), 1.6239708 (movie #1):
Minimum - Maximum: -4.18106 - 11.959
Average (Standard dev.): 2.39225e-09 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 128 128 128
Origin : 0 0 0
Limit : 127 127 127
Spacing : 128 128 128
Unit CellA = 406.4 A , B = 406.4 A , C = 406.4 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 3.175 A , Y = 3.175 A , Z = 3.175 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.1753.1753.175
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z406.400406.400406.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-20-28-19
NX/NY/NZ415638
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-4.18111.9590.000
Annotation DetailsRibosome structure from Desulfovibrio vulgaris Hildenborough (DvH)
Supplement
Sample
Name70S ribosome from Desulfovibrio vulgaris Hildenborough
Number of Components1
Oligomeric Statemonomer
Theoretical Mass3 MDa
Mass-estimation MethodSedimentaion
Experimental Mass3 MDa
Component #1: ribosome-prokaryote - Ribosome
Scientific nameRibosome
Theoretical Mass3 MDa
Experimental Mass3 MDa
ProkaryoteALL
Experiment
Sample Preparation
StainingThree microliter of 2% w/v uranyl acetate stain was applied to the EM grid for 1 min.
Specimen Conc0.03 mg/ml
Specimen Support Detailscarbon-coated and glow-discharged 300 mesh copper grid
Specimen Stateparticle
BufferDetails: 20mM Tris buffer with 60mM NH4Cl, 6mM MgCl2, 0.5mM EDTA and 1mM DTT
pH: 7.5
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 4000EX
Date08-Jul-2008
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage400 kV
Electron Dose17 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 40000 X, Calibrated: 40000 X
Astigmatismobjective lens astigmatism was corrected at 60,000 times magnification
Nominal Cs4.1 mm
Imaging ModeBRIGHT FIELD
Defocus600 nm - 2000 nm
Specimen Holder
HolderSide entry room T ( OTHER )
Tilt Angle0 degrees - 0 degrees
Temperature293 Kelvin
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images85
Sampling Size6.35 microns
Quant Bit Number8
DetailsThe images were scanned with a resolution of 6.35 micro m per pixel and later averaged 2 fold in each direction.
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmRefinement based on an initial model
SoftwareSPIDER
CTF CorrectionEach particle
Resolution By Author24
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections11000
Download
Data from EMDB
Header (meta data in XML format)emd-5041.xml (7.5 KB)
Map dataemd_5041.map.gz (6.9 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5041
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.4 KB