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- EMDB-1283: Molecular architecture and conformational flexibility of human RN... -

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Basic information

Entry
Database: EMDB / ID: 1283
TitleMolecular architecture and conformational flexibility of human RNA polymerase II.
Samplehuman RNA Polymerase II
SourceHomo sapiens / human
Map dataConformation 1
Methodsingle particle reconstruction, at 20 A resolution
AuthorsKostek SA / Grob P / De Carlo S / Lipscomb JS / Garczarek F / Nogales E
CitationStructure, 2006, 14, 1691-1700

Structure, 2006, 14, 1691-1700 StrPapers
Molecular architecture and conformational flexibility of human RNA polymerase II.
Seth A Kostek / Patricia Grob / Sacha De Carlo / J Slaton Lipscomb / Florian Garczarek / Eva Nogales

DateDeposition: Oct 28, 2006 / Header (metadata) release: Oct 28, 2006 / Map release: Oct 28, 2006 / Last update: Oct 28, 2006

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.32
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.32
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1283.map.gz (map file in CCP4 format, 6751 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
2.5 A/pix
= 300. A
120 pix
2.5 A/pix
= 300. A
120 pix
2.5 A/pix
= 300. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.5 A
Density
Contour Level:0.126, 0.32 (movie #1):
Minimum - Maximum-0.158582 - 0.587113
Average (Standard dev.)0.0115372 (0.0722153)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions120120120
Origin-60-60-60
Limit595959
Spacing120120120
CellA=B=C: 300 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.52.52.5
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean-0.1590.5870.012

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Supplemental data

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Sample components

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Entire human RNA Polymerase II

EntireName: human RNA Polymerase II / Oligomeric State: 12 subunit complex / Number of components: 12
MassTheoretical: 520 kDa / Experimental: 500 kDa

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Component #1: protein, Rpb1

ProteinName: Rpb1 / Number of Copies: 1 / Recombinant expression: No
MassExperimental: 220 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #2: protein, Rpb2

ProteinName: Rpb2 / Number of Copies: 1 / Recombinant expression: No
MassExperimental: 130 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #3: protein, Rpb3

ProteinName: Rpb3 / Recombinant expression: No / Number of Copies: 1
MassExperimental: 30 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #4: protein, Rpb4

ProteinName: Rpb4 / Number of Copies: 1 / Recombinant expression: No
MassExperimental: 20 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #5: protein, Rpb5

ProteinName: Rpb5 / Number of Copies: 1 / Recombinant expression: No
MassExperimental: 20 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #6: protein, Rpb6

ProteinName: Rpb6 / Recombinant expression: No / Number of Copies: 1
MassExperimental: 10 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #7: protein, Rpb7

ProteinName: Rpb7 / Recombinant expression: No / Number of Copies: 1
MassExperimental: 20 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #8: protein, Rpb8

ProteinName: Rpb8 / Recombinant expression: No / Number of Copies: 1
MassExperimental: 20 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #9: protein, Rpb9

ProteinName: Rpb9 / Number of Copies: 1 / Recombinant expression: No
MassExperimental: 10 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #10: protein, Rpb10

ProteinName: Rpb10 / Number of Copies: 1 / Recombinant expression: No
MassExperimental: 10 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #11: protein, Rpb11

ProteinName: Rpb11 / Number of Copies: 1 / Recombinant expression: No
MassExperimental: 10 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Component #12: protein, Rpb12

ProteinName: Rpb12 / Number of Copies: 1 / Recombinant expression: No
MassExperimental: 10 kDa
SourceSpecies: Homo sapiens / human
Source (natural)Organelle: Nucleus / Cell: HeLa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.01 mg/ml
Buffer solution: 200mM (NH4)2SO4, 25mM Hepes, 0.2M EDTA, 0.05% NP-40
pH: 7.9
Support film400 mesh copper grid
Stainingcryo-negative staining in a saturated solution of ammonium molybdate neutralized to a pH of 7.2. with 10 N NaOH
VitrificationCryogen name: ETHANE / Temperature: 90 K / Method: stained with ammonium molybdate before plunging

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50280 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3600 nm
Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN / Temperature: 90 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 19 / Scanner: OTHER / Sampling size: 6.3 microns / Bit depth: 14 / OD range: 1

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3406 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Fourier method / Software: FREALIGN / CTF correction: each micrograph / Resolution: 20 A / Resolution method: FSC 0.143

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