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- EMDB-5044: RNA polymerase structure : Structural survey of large protein com... -

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Basic information

Entry
Database: EMDB / ID: 5044
TitleRNA polymerase structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)
KeywordsRNA polymerase / Desulfovibrio vulgaris / DvH / transcription
SampleRNA polymerase from Desulfovibrio vulgaris Hildenborough
SourceDesulfovibrio vulgaris str. hildenborough / bacteria
Map dataRNA polymerase structure from Desulfovibrio vulgaris Hildenborough
Methodsingle particle reconstruction, at 19 A resolution
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
CitationProc. Natl. Acad. Sci. U.S.A., 2009, 106, 16580-16585

Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 16580-16585 StrPapers
Survey of large protein complexes in D. vulgaris reveals great structural diversity.
Bong-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

DateDeposition: Jan 9, 2009 / Header (metadata) release: Jan 21, 2009 / Map release: Sep 4, 2009 / Last update: Jan 9, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.8
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 1.8
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_5044.map.gz (map file in CCP4 format, 5789 KB)
Projections & slices
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Others
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.

Voxel sizeX=Y=Z: 3.18 A
Density
Contour Level:1.77 (by author), 1.8 (movie #1):
Minimum - Maximum-2.69486141 - 18.4408989
Average (Standard dev.)0E-8 (0.9999997)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions114114114
Origin000
Limit113113113
Spacing114114114
CellA=B=C: 362.52002 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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-20-28-19
NX/NY/NZ415638
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS114114114
D min/max/mean-2.69518.441-0.000

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Supplemental data

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Sample components

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Entire RNA polymerase from Desulfovibrio vulgaris Hildenborough

EntireName: RNA polymerase from Desulfovibrio vulgaris Hildenborough
Number of components: 6 / Oligomeric State: dimer
MassTheoretical: 885 kDa / Experimental: 885 kDa

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Component #1: protein, RNA polymerase

ProteinName: RNA polymerase / Oligomeric Details: dimer / Recombinant expression: No
MassTheoretical: 885 kDa / Experimental: 885 kDa
SourceSpecies: Desulfovibrio vulgaris str. hildenborough / bacteria
Source (natural)Location in cell: cytoplasmic

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.03 mg/ml / Buffer solution: 10 mM HEPES buffer / pH: 7
Support filmcarbon-coated and glow-discharged 300 mesh copper grid
StainingThree microliter of 2% w/v uranyl acetate stain was applied to the EM grid for 1 min.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 4000EX / Date: Mar 3, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 400 kV / Electron dose: 17 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 40000 X (nominal), 40000 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 60,000 times magnification
Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 2000 nm
Specimen HolderHolder: Side entry room T / Model: OTHER / Temperature: 293 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 33 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 8
Details: The images were scanned with a resolution of 6.35 micro m per pixel and later averaged 2 fold in each direction.

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 21420 / Applied symmetry: C2 (2 fold cyclic)
3D reconstructionAlgorithm: Refinement based on an initial model / Software: SPIDER / CTF correction: Each particle / Resolution: 19 A / Resolution method: FSC 0.5

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