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- EMDB-8137: Human core-PIC in the initial transcribing state -

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Entry
Database: EMDB / ID: 8137
TitleHuman core-PIC in the initial transcribing state
Map data
SampleHuman core-PIC in the initial transcribing state
  • RNA polymerase II
  • (General transcription ...) x 4
  • Super core promoter
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 12
  • (Transcription initiation factor ...) x 4
  • TATA-box-binding protein
  • Transcription elongation factor A protein 1
  • (nucleic-acidNucleic acid) x 2
  • (ligand) x 2
Function / homologyTBP domain superfamily / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Transcription factor IIA, helical / Transcription factor IIA, beta-barrel / HRDC-like superfamily / Transcription Factor IIF, Rap30/Rap74, interaction / 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 ...TBP domain superfamily / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Transcription factor IIA, helical / Transcription factor IIA, beta-barrel / HRDC-like superfamily / Transcription Factor IIF, Rap30/Rap74, interaction / 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 / RNA polymerases D / 30 to 40 Kd subunits signature. / Nucleic acid-binding, OB-fold / Zinc finger, RING/FYVE/PHD-type / Zinc finger, TFIIB-type / Transcription factor TFIIB, cyclin-like domain / Cyclin-like / RNA polymerase Rpb2, OB-fold / Transcription initiation factor IIF, alpha subunit / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase subunit RPB10 / Transcription factor TFIIB, conserved site / RNA-binding domain, S1 / Transcription factor TFIIE alpha subunit, C-terminal / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Transcription factor IIS, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / Transcription initiation factor TFIIE, beta subunit / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, C-terminal / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, subunit RPB6 / Transcription elongation factor, TFIIS / Transcription initiation factor IIE subunit alpha, N-terminal / S1 domain / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIF, beta subunit / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Transcription elongation factor S-II, central domain / Transcription factor IIA, alpha/beta subunit / RNA polymerase, Rpb8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase subunit RPB4/RPC9 / RNA polymerase Rpb7, N-terminal / RNA polymerase, subunit omega/K/RPB6 / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb4/RPC9, core / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb1, domain 4 / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / TFIIEalpha/SarR/Rpc3 HTH domain / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase beta subunit / TFIIE alpha subunit / RNA polymerases M/15 Kd subunit / TFIIE beta subunit core domain / Transcription initiation factor IIA, gamma subunit, helical domain / TFIIF, beta subunit HTH domain / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha/beta subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / 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 Rpb2, domain 3 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb3/Rpb11 dimerisation domain / C-terminal general transcription factor TFIIE alpha / TFIIS helical bundle-like domain / TFIIB zinc-binding / Transcription factor S-II (TFIIS), central domain / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 6
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsHe Y / Yan C / Fang J / Inouye C / Tjian R / Ivanov I / Nogales E
CitationJournal: Nature / Year: 2016
Title: Near-atomic resolution visualization of human transcription promoter opening.
Authors: Yuan He / Chunli Yan / Jie Fang / Carla Inouye / Robert Tjian / Ivaylo Ivanov / Eva Nogales
Validation ReportPDB-ID: 5iyc

SummaryFull reportAbout validation report
DateDeposition: May 2, 2016 / Header (metadata) release: May 18, 2016 / Map release: May 18, 2016 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5iyc
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8137.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.31 Å/pix.
= 503.04 Å
384 pix
1.31 Å/pix.
= 503.04 Å
384 pix
1.31 Å/pix.
= 503.04 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:0.01 (by author), 0.01 (movie #1):
Minimum - Maximum-0.10279353 - 0.16405329
Average (Standard dev.)0.00008211587 (0.0021512734)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.00.00.0
Limit383.0383.0383.0
Spacing384384384
CellA=B=C: 503.03998 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/z384384384
origin x/y/z0.0000.0000.000
length x/y/z503.040503.040503.040
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ329329329
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1030.1640.000

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Supplemental data

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Sample components

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Entire Human core-PIC in the initial transcribing state

EntireName: Human core-PIC in the initial transcribing state / Number of components: 29

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Component #1: protein, Human core-PIC in the initial transcribing state

ProteinName: Human core-PIC in the initial transcribing state / Recombinant expression: No
MassTheoretical: 900 kDa
SourceSpecies: Homo sapiens (human)

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Component #2: protein, RNA polymerase II

ProteinName: RNA polymerase II / Recombinant expression: No
MassTheoretical: 520 kDa
SourceSpecies: Homo sapiens (human)

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Component #3: protein, General transcription factors

ProteinName: General transcription factorsGeneral transcription factor
Recombinant expression: No
MassTheoretical: 330 kDa
SourceSpecies: Homo sapiens (human)

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Component #4: protein, Super core promoter

ProteinName: Super core promoter / Recombinant expression: No
MassTheoretical: 60 kDa
SourceSpecies: Homo sapiens (human)

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

ProteinName: DNA-directed RNA polymerase II subunit RPB1Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 217.420047 kDa
SourceSpecies: Human (human)

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Component #6: 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 #7: 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 #8: 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 #9: protein, DNA-directed RNA polymerase II subunit RPB5

ProteinName: DNA-directed RNA polymerase II subunit RPB5Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.584223 kDa
SourceSpecies: Human (human)

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Component #10: protein, DNA-directed RNA polymerase II subunit RPB6

ProteinName: DNA-directed RNA polymerase II subunit RPB6Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.491026 kDa
SourceSpecies: Human (human)

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Component #11: 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 #12: protein, DNA-directed RNA polymerase II subunit RPB8

ProteinName: DNA-directed RNA polymerase II subunit RPB8Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.162273 kDa
SourceSpecies: Human (human)

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Component #13: 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 #14: protein, DNA-directed RNA polymerase II subunit RPB10

ProteinName: DNA-directed RNA polymerase II subunit RPB10Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.655123 kDa
SourceSpecies: Human (human)

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Component #15: 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 #16: protein, DNA-directed RNA polymerase II subunit RPB12

ProteinName: DNA-directed RNA polymerase II subunit RPB12Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.018244 kDa
SourceSpecies: Human (human)

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Component #17: protein, Transcription initiation factor IIB

ProteinName: Transcription initiation factor IIB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.877949 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #18: protein, Transcription initiation factor IIA subunit 1

ProteinName: Transcription initiation factor IIA subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.544551 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #19: protein, Transcription initiation factor IIA subunit 2

ProteinName: Transcription initiation factor IIA subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.469091 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #20: protein, TATA-box-binding protein

ProteinName: TATA-box-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.729938 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #21: protein, General transcription factor IIE subunit 1

ProteinName: General transcription factor IIE subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.516094 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #22: protein, Transcription initiation factor IIE subunit beta

ProteinName: Transcription initiation factor IIE subunit beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.106824 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #23: protein, General transcription factor IIF subunit 1

ProteinName: General transcription factor IIF subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.343578 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #24: protein, General transcription factor IIF subunit 2

ProteinName: General transcription factor IIF subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.427309 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #25: protein, Transcription elongation factor A protein 1

ProteinName: Transcription elongation factor A protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.022723 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #26: nucleic-acid, SCP-X

Nucleic-acidName: SCP-X / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DA)(DA)(DG)(DG)(DG)(DC)(DG)(DC)(DC) (DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DG)(DG) (DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DC)(DG)(DA)(DA)(DC)(DA)(DC)(DT)(DC)(DG) (DA)(DG)(DC)(DC)(DG)(DA)(DG)(DC)(DA)(DG) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DA)(DC)
MassTheoretical: 24.800826 kDa
SourceSpecies: Homo sapiens (human)

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Component #27: nucleic-acid, SCP-Y

Nucleic-acidName: SCP-Y / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DT)(DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT) (DC)(DT)(DG)(DC)(DT)(DC)(DG)(DG)(DC)(DT) (DC)(DG)(DA)(DG)(DT)(DG)(DT)(DT)(DC)(DG) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DT)(DG) (DA)(DG)(DG)(DA)(DC)(DG)(DA)(DA)(DC)(DG) (DC)(DG)(DC)(DC)(DC)(DC)(DC)(DA)(DC)(DC) (DC)(DC)(DC)(DT)(DT)(DT)(DT)(DA)(DT)(DA) (DG)(DG)(DC)(DG)(DC)(DC)(DC)(DT)(DT)(DC)
MassTheoretical: 24.513598 kDa
SourceSpecies: Homo sapiens (human)

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Component #28: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #29: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 11 / 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.: 0.3 mg/ml / pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV)..

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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: 42 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 27500.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4000.0 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 90590
3D reconstructionSoftware: RELION / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible
Output model

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