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

by single particle reconstruction, at 19 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.8, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1.8, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5044
TitleRNA polymerase structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)
MapRNA polymerase structure from Desulfovibrio vulgaris Hildenborough
SampleRNA polymerase from Desulfovibrio vulgaris Hildenborough
KeywordsRNA polymerase, Desulfovibrio vulgaris, DvH, transcription
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: 2009-01-09, Header release: 2009-01-21, Map release: 2009-09-04, Last update: 2013-12-11
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.8, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1.8, Image by UCSF CHIMERA

Supplemental images
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Related Structure Data
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Cite: data citing same article

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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_5044.map.gz ( map file in CCP4 format, 5789 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
114 pix
3.18 A/pix
= 362.52 A
114 pix
3.18 A/pix
= 362.52 A
114 pix
3.18 A/pix
= 362.52 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1.77 (by author), 1.8 (movie #1):
Minimum - Maximum: -2.69486141 - 18.4408989
Average (Standard dev.): 0E-8 (0.9999997)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions114114114
Origin000
Limit113113113
Spacing114114114
Unit CellA= B= C: 362.52002 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.18 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.183.183.18
M x/y/z114114114
origin x/y/z0.0000.0000.000
length x/y/z362.520362.520362.520
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-160-160-159
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS114114114
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-2.69518.441-0.000
Annotation DetailsRNA polymerase structure from Desulfovibrio vulgaris Hildenborough
Supplement
Images
Images
Sample
NameRNA polymerase from Desulfovibrio vulgaris Hildenborough
Number of Components6
Oligomeric Statedimer
Theoretical Mass0.885MDa
Experimental Mass0.885MDa
Component #1: protein - RNA polymerase
Scientific nameRNA polymerase
Theoretical Mass0.885 MDa
Experimental Mass0.885 MDa
Oligomeric Detailsdimer
Scientific Name of SpeciesDesulfovibrio vulgaris str. Hildenborough
NCBI taxonomy882
Recombinant expressionNo
Natural SourceCell Location: cytoplasmic
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: 10 mM HEPES buffer
pH: 7
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 4000EX
Date03-Mar-2008
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage400 kV
Electron Dose17 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 40000, Calibrated: 40000
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
ModelOTHER
Tilt Angle0 degrees - 0 degrees
Temperature293 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images33
Sampling Size6.35
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
3D reconstruction
AlgorithmRefinement based on an initial model
SoftwareSPIDER
CTF CorrectionEach particle
Resolution By Author19 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections21420
Applied SymmetryC2 (2 fold cyclic)
Download
Data from EMDB
Header (meta data in XML format)emd-5044.xml (7.7 KB)
Map dataemd_5044.map.gz (4.8 MB)
Imagesemd_5044_1.jpg (40.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5044
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 25.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 25.8 KB