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- EMDB-3817: Structure of an RNA polymerase II-DSIF transcription elongation c... -

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Basic information

Entry
Database: EMDB / ID: 3817
TitleStructure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC3
SampleRNA polymerase II-DSIF elongation complex
SourceHomo sapiens / human
Bos taurus / mammal / ウシ /
Synthetic construct
Map dataLocally filtered map, B-factor 0
Methodsingle particle reconstruction, at 3.7 Å resolution
AuthorsBernecky C / Plitzko JM / Cramer P
CitationNat. Struct. Mol. Biol., 2017

Nat. Struct. Mol. Biol., 2017 StrPapers
Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.
Carrie Bernecky / Jürgen M Plitzko / Patrick Cramer

Validation ReportPDB-ID: 5oik

SummaryFull reportAbout validation report
DateDeposition: Jul 18, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Sep 13, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.022
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5oik
  • Surface level: 0.022
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3817.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.35 Å/pix.
= 345.6 Å
256 pix
1.35 Å/pix.
= 345.6 Å
256 pix
1.35 Å/pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.022 (by author), 0.022 (movie #1):
Minimum - Maximum-0.05270735 - 0.15260181
Average (Standard dev.)-1.2683433E-5 (0.005105959)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 345.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0530.153-0.000

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Supplemental data

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Mask #1

Fileemd_3817_msk_1.map ( map file in CCP4 format, 67109 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsNone
Space group number1

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Mask #1~

Fileemd_3817_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire RNA polymerase II-DSIF elongation complex

EntireName: RNA polymerase II-DSIF elongation complex / Number of components: 23
MassTheoretical: 130 kDa

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Component #1: protein, RNA polymerase II-DSIF elongation complex

ProteinName: RNA polymerase II-DSIF elongation complex / Recombinant expression: No
MassTheoretical: 130 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: BL21(DE3)

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Component #2: protein, RNA polymerase II

ProteinName: RNA polymerase II / Recombinant expression: No
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #3: protein, DSIF

ProteinName: DSIF / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: BL21(DE3)

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Component #4: protein, DNA-RNA synthetic construct

ProteinName: DNA-RNA synthetic construct / Recombinant expression: No
SourceSpecies: Synthetic construct
Source (engineered)Expression System: Synthetic construct

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Component #5: protein, DNA-directed RNA polymerase II subunit RPB1

ProteinName: DNA-directed RNA polymerase II subunit RPB1 / Recombinant expression: No
MassTheoretical: 217.436062 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #6: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit beta / Recombinant expression: No
MassTheoretical: 134.041422 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #7: protein, DNA-directed RNA polymerase II subunit RPB3

ProteinName: DNA-directed RNA polymerase II subunit RPB3 / Recombinant expression: No
MassTheoretical: 31.466098 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #8: protein, Polymerase (RNA) II (DNA directed) polypeptide D

ProteinName: Polymerase (RNA) II (DNA directed) polypeptide D / Recombinant expression: No
MassTheoretical: 16.347255 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
Recombinant expression: No
MassTheoretical: 24.514219 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #10: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
Recombinant expression: No
MassTheoretical: 14.491026 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #11: protein, DNA-directed RNA polymerase II subunit RPB7

ProteinName: DNA-directed RNA polymerase II subunit RPB7 / Recombinant expression: No
MassTheoretical: 19.314283 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #12: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 17.162273 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #13: protein, DNA-directed RNA polymerase II subunit RPB9

ProteinName: DNA-directed RNA polymerase II subunit RPB9 / Recombinant expression: No
MassTheoretical: 14.507205 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #14: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
Recombinant expression: No
MassTheoretical: 7.655123 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #15: protein, DNA-directed RNA polymerase II subunit RPB11

ProteinName: DNA-directed RNA polymerase II subunit RPB11 / Recombinant expression: No
MassTheoretical: 13.310284 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #16: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
Recombinant expression: No
MassTheoretical: 7.018244 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #17: nucleic-acid, DNA (43-MER)

Nucleic-acidName: DNA (43-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DG)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DA) (DG)(DT)(DA)(DT)(DT)(DC)(DT)(DA)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DA)(DG)(DT)(DA) (DC)(DT)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DG) (DA)(DT)(DC)
MassTheoretical: 13.303563 kDa

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Component #18: nucleic-acid, RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*...

Nucleic-acidName: RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3')
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UAACGAGAUC AUAACAUUUG AACAAGAAUA UAUAUACAUA AAGACCAGGC
MassTheoretical: 16.081696 kDa

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Component #19: nucleic-acid, DNA (43-MER)

Nucleic-acidName: DNA (43-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DA)(DT)(DC)(DA)(DA)(DG)(DC)(DT)(DC) (DA)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DA)(DA) (DG)(DC)(DC)(DT)(DG)(DG)(DT)(DC)(DT)(DA) (DT)(DA)(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT) (DG)(DC)(DC)
MassTheoretical: 13.178483 kDa

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Component #20: protein, Transcription elongation factor SPT4

ProteinName: Transcription elongation factor SPT4 / Recombinant expression: No
MassTheoretical: 13.210201 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #21: protein, Transcription elongation factor SPT5

ProteinName: Transcription elongation factor SPT5 / Recombinant expression: No
MassTheoretical: 121.145477 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #22: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #23: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.25 mg/ml / Buffer solution: pH was adjusted at 25 degrees Celsius / pH: 7.25
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid 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: 33 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37000 X (nominal), 37037 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 3600 nm / Energy filter: GIF Quantum / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2549
Details: Movies were aligned and binned to the physical pixel size of 1.35 angstroms.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 101140
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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