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- EMDB-7997: RNA Pol II(G) -

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Basic information

Entry
Database: EMDB / ID: 7997
TitleRNA Pol II(G)
Map dataRNA Pol II(G)
SamplehPolII_Gdown1
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 8
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • ligand
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsYu X / Jishage M / Shi Y / Ganesan S / Sali A / Chait BT / Asturias F / Roeder RG
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1.
Authors: Miki Jishage / Xiaodi Yu / Yi Shi / Sai J Ganesan / Wei-Yi Chen / Andrej Sali / Brian T Chait / Francisco J Asturias / Robert G Roeder
DateDeposition: Jun 11, 2018 / Header (metadata) release: Jul 25, 2018 / Map release: Oct 17, 2018 / Last update: Oct 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7997.map.gz (map file in CCP4 format, 44958 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
224 pix
1.31 Å/pix.
= 293.44 Å
224 pix
1.31 Å/pix.
= 293.44 Å
224 pix
1.31 Å/pix.
= 293.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.13978457 - 0.23811144
Average (Standard dev.)0.0006405608 (0.006816815)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions224224224
Origin0.00.00.0
Limit223.0223.0223.0
Spacing224224224
CellA=B=C: 293.44 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z293.440293.440293.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.1400.2380.001

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Supplemental data

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Sample components

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Entire hPolII_Gdown1

EntireName: hPolII_Gdown1 / Number of components: 15

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Component #1: protein, hPolII_Gdown1

ProteinName: hPolII_Gdown1 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, DNA-directed RNA polymerase II subunit RPB1

ProteinName: DNA-directed RNA polymerase II subunit RPB1Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 217.450078 kDa
SourceSpecies: Human (human)

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Component #3: protein, DNA-directed RNA polymerase II subunit RPB2

ProteinName: DNA-directed RNA polymerase II subunit RPB2Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 134.071453 kDa
SourceSpecies: Human (human)

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Component #4: protein, DNA-directed RNA polymerase II subunit RPB3

ProteinName: DNA-directed RNA polymerase II subunit RPB3Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.478148 kDa
SourceSpecies: Human (human)

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Component #5: protein, DNA-directed RNA polymerase II subunit RPB4

ProteinName: DNA-directed RNA polymerase II subunit RPB4Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.331255 kDa
SourceSpecies: Human (human)

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Component #6: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.659291 kDa
SourceSpecies: Human (human)

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Component #7: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.491026 kDa
SourceSpecies: Human (human)

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Component #8: protein, DNA-directed RNA polymerase II subunit RPB7

ProteinName: DNA-directed RNA polymerase II subunit RPB7Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.314283 kDa
SourceSpecies: Human (human)

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Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.162273 kDa
SourceSpecies: Human (human)

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Component #10: protein, DNA-directed RNA polymerase II subunit RPB9

ProteinName: DNA-directed RNA polymerase II subunit RPB9Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.541221 kDa
SourceSpecies: Human (human)

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Component #11: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.655123 kDa
SourceSpecies: Human (human)

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Component #12: protein, DNA-directed RNA polymerase II subunit RPB11-a

ProteinName: DNA-directed RNA polymerase II subunit RPB11-aPolymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.310284 kDa
SourceSpecies: Human (human)

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Component #13: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.018244 kDa
SourceSpecies: Human (human)

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Component #14: protein, DNA-directed RNA polymerase II subunit GRINL1A

ProteinName: DNA-directed RNA polymerase II subunit GRINL1APolymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.756896 kDa
SourceSpecies: Human (human)

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Component #15: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionpH: 7.5
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 141619
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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