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- EMDB-6747: RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS -

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Entry
Database: EMDB / ID: 6747
TitleRNA Polymerase II elongation complex bound with Spt4/5 and TFIIS
Map dataconsensus map after sharpening
SampleRNA polymerase II elongation complex bound with Spt4/5 and TFIIS
  • (RNA polymerase ...) x 10
  • Spt4/5 and TFIIS
  • (DNA-directed RNA polymerase ...Polymerase) x 3
  • (nucleic-acidNucleic acid) x 3
  • General transcription elongation factor TFIIS
  • Transcription elongation factor SPT4
  • Protein that forms a complex with Spt4p
  • (ligand) x 2
Function / homologyDNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Ribosomal protein L2, domain 2 / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit 2 / Transcription elongation factor Spt5 / Transcription factor IIS, N-terminal / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit ...DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Ribosomal protein L2, domain 2 / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit 2 / Transcription elongation factor Spt5 / Transcription factor IIS, N-terminal / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / Spt5 transcription elongation factor, N-terminal / Spt4/RpoE2 zinc finger / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase subunit/transcription factor S / Transcription elongation factor, IIS-type / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / Translation protein SH3-like domain superfamily / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Transcription initiation Spt4 / HRDC-like superfamily / DNA-directed RNA polymerase, insert domain / Pol II subunit B9, C-terminal zinc ribbon / TFIIS/LEDGF domain superfamily / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases N / 8 kDa subunit / 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 Rpb8 / RNA polymerase Rpb5, N-terminal domain / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb5, C-terminal domain / 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 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb6 / Transcription factor S-II (TFIIS) / RPB5-like RNA polymerase subunit / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RPB6/omega subunit-like superfamily / Transcription elongation factor S-II, central domain superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / NusG, N-terminal domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase RBP11 / RNA polymerase Rpb1, funnel domain superfamily / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / KOW motif / RNA polymerase Rpb2, domain 6 / S1 RNA binding domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 3 / Spt4/RpoE2 zinc finger / Transcription factor S-II (TFIIS), central domain / TFIIS helical bundle-like domain / Spt5 transcription elongation factor, acidic N-terminal / RNA polymerase Rpb3/Rpb11 dimerisation domain / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerases M / 15 Kd subunits signature. / RNA polymerase Rpb1, domain 5 / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / S1 domain profile. / Zinc finger TFIIS-type profile.
Function and homology information
SourceKomagataella pastoris (fungus) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Methodsingle particle reconstruction / cryo EM / 3.83 Å resolution
AuthorsEhara H / Yokoyama T
CitationJournal: Science / Year: 2017
Title: Structure of the complete elongation complex of RNA polymerase II with basal factors.
Authors: Haruhiko Ehara / Takeshi Yokoyama / Hideki Shigematsu / Shigeyuki Yokoyama / Mikako Shirouzu / Shun-Ichi Sekine
Abstract: In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we ...In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes.
Copyright: 2017, American Association for the Advancement of Science.
Validation ReportPDB-ID: 5xon

SummaryFull reportAbout validation report
DateDeposition: May 29, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Aug 16, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0666
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0666
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xon
  • Surface level: 0.0666
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6747.map.gz (map file in CCP4 format, 23329 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
1.53 Å/pix.
= 275.94 Å
180 pix
1.53 Å/pix.
= 275.94 Å
180 pix
1.53 Å/pix.
= 275.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.533 Å
Density
Contour Level:0.0666 (by author), 0.0666 (movie #1):
Minimum - Maximum-0.28849798 - 0.5025477
Average (Standard dev.)0.0017449913 (0.016120026)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin000
Limit179179179
Spacing180180180
CellA=B=C: 275.94 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5331.5331.533
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z275.940275.940275.940
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.2880.5030.002

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Supplemental data

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Sample components

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Entire RNA polymerase II elongation complex bound with Spt4/5 and TFIIS

EntireName: RNA polymerase II elongation complex bound with Spt4/5 and TFIIS
Number of components: 23

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Component #1: protein, RNA polymerase II elongation complex bound with Spt4/5 a...

ProteinName: RNA polymerase II elongation complex bound with Spt4/5 and TFIIS
Recombinant expression: No
SourceSpecies: Komagataella pastoris (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, RNA polymerase II

ProteinName: RNA polymerase II / Recombinant expression: No

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Component #3: protein, Spt4/5 and TFIIS

ProteinName: Spt4/5 and TFIIS / Recombinant expression: No

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

ProteinName: DNA-directed RNA polymerase subunit / Recombinant expression: No
MassTheoretical: 194.107422 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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

ProteinName: DNA-directed RNA polymerase subunit beta / Recombinant expression: No
MassTheoretical: 139.746094 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #6: protein, RNA polymerase II third largest subunit B44, part of cen...

ProteinName: RNA polymerase II third largest subunit B44, part of central core
Recombinant expression: No
MassTheoretical: 34.216293 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #7: protein, RNA polymerase II subunit B32

ProteinName: RNA polymerase II subunit B32 / Recombinant expression: No
MassTheoretical: 20.62298 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #8: protein, RNA polymerase subunit ABC27, common to RNA polymerases ...

ProteinName: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
Recombinant expression: No
MassTheoretical: 24.96268 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #9: protein, RNA polymerase subunit ABC23, common to RNA polymerases ...

ProteinName: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
Recombinant expression: No
MassTheoretical: 17.803588 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #10: protein, RNA polymerase II subunit

ProteinName: RNA polymerase II subunit / Recombinant expression: No
MassTheoretical: 18.802625 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #11: protein, RNA polymerase subunit ABC14.5, common to RNA polymerase...

ProteinName: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
Recombinant expression: No
MassTheoretical: 16.24922 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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

ProteinName: DNA-directed RNA polymerase subunit / Recombinant expression: No
MassTheoretical: 13.61232 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #13: protein, RNA polymerase subunit ABC10-beta, common to RNA polymer...

ProteinName: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
Recombinant expression: No
MassTheoretical: 8.554064 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #14: protein, RNA polymerase II subunit B12.5

ProteinName: RNA polymerase II subunit B12.5 / Recombinant expression: No
MassTheoretical: 13.832896 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #15: protein, RNA polymerase subunit, found in RNA polymerase complexe...

ProteinName: RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
Recombinant expression: No
MassTheoretical: 7.862048 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #16: nucleic-acid, RNA (30-MER)

Nucleic-acidName: RNA (30-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUCUUGAAUC UAUUUCUUUU AUCGAGAGGU
MassTheoretical: 9.492561 kDa

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Component #17: nucleic-acid, DNA (48-MER)

Nucleic-acidName: DNA (48-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DC)(DC)(DG) (DA)(DT)(DA)(DA)(DG)(DC)(DA)(DG)(DA)(DC) (DG)(DT)(DA)(DC)(DC)(DT)(DC)(DT)(DC)(DG) (DA)(DC)(DC)(DC)(DT)(DG)(DT)(DG)(DC)(DT) (DA)(DG)(DA)(DC)(DA)(DC)(DG)(DG)
MassTheoretical: 14.659406 kDa

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Component #18: nucleic-acid, DNA (48-MER)

Nucleic-acidName: DNA (48-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DC)(DG)(DT)(DG)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DG)(DA)(DA)(DA) (DT)(DG)(DG)(DT)(DT)(DT)(DG)(DT)(DG)(DT) (DC)(DT)(DG)(DC)(DT)(DT)(DA)(DT)(DC)(DG) (DG)(DT)(DA)(DG)(DA)(DG)(DT)(DG)
MassTheoretical: 14.917541 kDa

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Component #19: protein, General transcription elongation factor TFIIS

ProteinName: General transcription elongation factor TFIIS / Recombinant expression: No
MassTheoretical: 21.694734 kDa
Source (engineered)Expression System: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #20: protein, Transcription elongation factor SPT4

ProteinName: Transcription elongation factor SPT4 / Recombinant expression: No
MassTheoretical: 12.039614 kDa
Source (engineered)Expression System: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #21: protein, Protein that forms a complex with Spt4p

ProteinName: Protein that forms a complex with Spt4p / Recombinant expression: No
MassTheoretical: 68.283984 kDa
Source (engineered)Expression System: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864

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Component #22: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 10 / 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

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3607

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 682749
3D reconstructionSoftware: RELION / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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