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- EMDB-0038: Structure of paused transcription complex Pol II-DSIF-NELF -

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Entry
Database: EMDB / ID: 0038
TitleStructure of paused transcription complex Pol II-DSIF-NELF
Map dataGlobally refined overall PEC map (Map 1).
SampleRNA Polymerase II elongation complex bound to DSIF and NELF
  • Sus scrofa RNA Polymerase II
  • (Negative elongation factor ...) x 5
  • DRB sensitivity inducing factor (DSIF)
  • HIV-1 pause transcription scaffold
  • (DNA-directed RNA polymerase ...Polymerase) x 3
  • (RNA polymerase II subunit ...) x 5
  • DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
  • (Uncharacterized ...) x 3
  • (nucleic-acidNucleic acid) x 3
  • (Transcription elongation factor ...) x 2
  • (ligand) x 2
Function / homologyRNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, subunit RPB6 / Pausing and recovery of HIV elongation / Negative elongation factor E / Pol II subunit B9, C-terminal zinc ribbon / Negative elongation factor E, RNA recognition motif / RPB5-like RNA polymerase subunit superfamily / RNA-binding domain superfamily / RPB6/omega subunit-like superfamily ...RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, subunit RPB6 / Pausing and recovery of HIV elongation / Negative elongation factor E / Pol II subunit B9, C-terminal zinc ribbon / Negative elongation factor E, RNA recognition motif / RPB5-like RNA polymerase subunit superfamily / RNA-binding domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain superfamily / Spt5 C-terminal domain / RNA polymerase Rpb5, N-terminal domain superfamily / NusG, N-terminal domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / Hepatitis delta antigen (HDAg) domain / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / Spt4 superfamily / Negative elongation factor A / RNA-binding domain, S1 / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Nucleotide-binding alpha-beta plait domain superfamily / Transcription initiation Spt4 / Cofactor of BRCA1 / HRDC-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Spt4/RpoE2 zinc finger / Ribosomal protein L2, domain 2 / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit 2 / Transcription elongation factor Spt5, eukaryote / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Spt5 transcription elongation factor, N-terminal / NGN domain, eukaryotic / KOW motif / Translation protein SH3-like domain superfamily / Zinc finger TFIIS-type profile. / RNA polymerases D / 30 to 40 Kd subunits signature. / Zinc finger TFIIS-type signature. / RNA polymerases M / 15 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / Eukaryotic RNA Recognition Motif (RRM) profile. / Hepatitis delta antigen (HDAg) domain profile. / Spt5 transcription elongation factor, acidic N-terminal / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Formation of HIV elongation complex in the absence of HIV Tat / Formation of the HIV-1 Early Elongation Complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / Formation of HIV-1 elongation complex containing HIV-1 Tat / Pausing and recovery of Tat-mediated HIV elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / Tat-mediated HIV elongation arrest and recovery / RNA polymerase Rpb3/Rpb11 dimerisation domain / Cofactor of BRCA1 (COBRA1) / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb8 / S1 RNA binding domain / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases M/15 Kd subunit / Early transcription elongation factor of RNA pol II, NGN section / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb5, N-terminal domain / Spt4/RpoE2 zinc finger / RNA polymerase Rpb4 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / TH1 protein / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / HIV elongation arrest and recovery / mRNA Splicing - Minor Pathway / RNA polymerase Rpb2, domain 5 / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs
Function and homology information
SourceSus scrofa (pig) / Homo sapiens (human) / Human immunodeficiency virus 1 / Pig (pig)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsVos SM / Farnung L / Urlaub H / Cramer P
CitationJournal: Nature / Year: 2018
Title: Structure of paused transcription complex Pol II-DSIF-NELF.
Authors: Seychelle M Vos / Lucas Farnung / Henning Urlaub / Patrick Cramer
Validation ReportPDB-ID: 6gml

SummaryFull reportAbout validation report
DateDeposition: May 27, 2018 / Header (metadata) release: Sep 5, 2018 / Map release: Sep 5, 2018 / Last update: Oct 3, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6gml
  • Surface level: 0.00596
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0038.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
1.23 Å/pix.
= 314.291 Å
256 pix
1.23 Å/pix.
= 314.291 Å
256 pix
1.23 Å/pix.
= 314.291 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2277 Å
Density
Contour Level:0.00596 (by author), 0.007 (movie #1):
Minimum - Maximum-0.016329648 - 0.042056307
Average (Standard dev.)0.000112259506 (0.0017798187)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 314.2912 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.227699218751.227699218751.22769921875
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z314.291314.291314.291
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-0.0160.0420.000

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Supplemental data

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Mask #1

Fileemd_0038_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 elongation complex bound to DSIF and NELF

EntireName: RNA Polymerase II elongation complex bound to DSIF and NELF
Number of components: 28

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Component #1: protein, RNA Polymerase II elongation complex bound to DSIF and NELF

ProteinName: RNA Polymerase II elongation complex bound to DSIF and NELF
Recombinant expression: No
MassTheoretical: 927.1 kDa

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Component #2: protein, Sus scrofa RNA Polymerase II

ProteinName: Sus scrofa RNA Polymerase II / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

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Component #3: protein, Negative elongation factor (NELF)

ProteinName: Negative elongation factor (NELF) / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #4: protein, DRB sensitivity inducing factor (DSIF)

ProteinName: DRB sensitivity inducing factor (DSIF) / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #5: protein, HIV-1 pause transcription scaffold

ProteinName: HIV-1 pause transcription scaffold / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: synthetic construct (others)

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

ProteinName: DNA-directed RNA polymerase subunitPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 217.551156 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Thymus

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

ProteinName: DNA-directed RNA polymerase subunit betaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 134.041422 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Thymus

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Component #8: protein, RNA polymerase II subunit C

ProteinName: RNA polymerase II subunit C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.997557 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Thymus

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Component #9: protein, RNA polymerase II subunit E

ProteinName: RNA polymerase II subunit E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.644318 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Thymus

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Component #10: protein, RNA polymerase II subunit F

ProteinName: RNA polymerase II subunit F / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.477001 kDa
SourceSpecies: Pig (pig)

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Component #11: 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: Pig (pig)
Source (natural)Organ or tissue: Thymus

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Component #12: 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: Pig (pig)
Source (natural)Organ or tissue: Thymus

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Component #13: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.702517 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Thymus

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Component #14: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.310284 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Thymus

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Component #15: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.018244 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Thymus

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Component #16: nucleic-acid, Non-template DNA

Nucleic-acidName: Non-template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DT)(DA)(DC)(DA)(DC)(DT)(DA)(DG)(DT) (DA)(DC)(DC)(DT)(DA)(DC)(DT)(DC)(DG)(DA) (DG)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DA)(DA) (DG)(DC)(DC)(DT)(DC)(DA)(DA)(DT)(DA)(DA) (DA)(DG)(DC)(DT)(DT)(DG)(DC)(DC)
MassTheoretical: 14.712466 kDa
SourceSpecies: Human immunodeficiency virus 1

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Component #17: nucleic-acid, TAR RNA

Nucleic-acidName: TAR RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
ACCAGAUCUG AGCCUGGGAG CUCUCUGGCU AACUAGGGAA CCCACU
MassTheoretical: 14.746812 kDa
SourceSpecies: Human immunodeficiency virus 1

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Component #18: nucleic-acid, Template DNA

Nucleic-acidName: Template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DG)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DT) (DA)(DT)(DT)(DG)(DA)(DG)(DG)(DC)(DT)(DT) (DA)(DA)(DG)(DC)(DA)(DG)(DT)(DG)(DG)(DG) (DT)(DT)(DC)(DC)(DA)(DG)(DG)(DT)(DA)(DC) (DT)(DA)(DG)(DT)(DG)(DT)(DA)(DC)
MassTheoretical: 14.910556 kDa
SourceSpecies: Human immunodeficiency virus 1

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Component #19: protein, Negative elongation factor A

ProteinName: Negative elongation factor A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.343598 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #20: protein, Negative elongation factor B

ProteinName: Negative elongation factor B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.57723 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #21: protein, Negative elongation factor C/D

ProteinName: Negative elongation factor C/D / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.651746 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #22: protein, Negative elongation factor E

ProteinName: Negative elongation factor E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.363449 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #23: protein, Transcription elongation factor SPT4

ProteinName: Transcription elongation factor SPT4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.555891 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #24: protein, Transcription elongation factor SPT5

ProteinName: Transcription elongation factor SPT5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 121.145477 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #25: protein, RNA polymerase II subunit D

ProteinName: RNA polymerase II subunit D / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.331255 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Thymus

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Component #26: protein, RNA polymerase II subunit G

ProteinName: RNA polymerase II subunit G / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.314283 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Thymus

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Component #27: ligand, MAGNESIUM ION

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

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Component #28: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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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: 46 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 165000.0 X (nominal) / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 11740

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 162269
3D reconstructionSoftware: RELION / Resolution: 3.2 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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