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- EMDB-9961: Thermococcus kodakarensis RNA polymerase in complex with transcri... -

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Basic information

Entry
Database: EMDB / ID: EMD-9961
TitleThermococcus kodakarensis RNA polymerase in complex with transcription factor E
Map data
SampleThermococcus kodakarensis RNA polymerase in complex with transcription factor E
Function / homology
Function and homology information


transcription open complex formation at RNA polymerase II promoter / RNA polymerase complex / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription, DNA-templated / protein dimerization activity / nucleotide binding / regulation of transcription, DNA-templated ...transcription open complex formation at RNA polymerase II promoter / RNA polymerase complex / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription, DNA-templated / protein dimerization activity / nucleotide binding / regulation of transcription, DNA-templated / DNA binding / zinc ion binding / metal ion binding
Similarity search - Function
Transcription factor TFE, archaea / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase, subunit E/RPC8 / TFIIEalpha/SarR/Rpc3 HTH domain ...Transcription factor TFE, archaea / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase, subunit E/RPC8 / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription initiation factor IIE subunit alpha, N-terminal / TFIIE alpha subunit / Transcription factor E / Transcription factor TFE/TFIIEalpha HTH domain / Transcription initiation factor IIE / TFE/IIEalpha-type HTH domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 kDa subunit / RNA polymerase subunit RPB10 / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase subunit CX / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / : / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase Rpb5, C-terminal domain / RPB5-like RNA polymerase subunit superfamily / : / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerases K / 14 to 18 Kd subunits signature. / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA-binding domain, S1 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / : / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb1, domain 4 / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 2 / RNA polymerase, alpha subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerases D / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 3 / DNA-directed RNA polymerase, subunit 2 / RNA polymerases beta chain signature. / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb2, domain 7 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / Winged helix DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase, subunit E / DNA-directed RNA polymerase, subunit F / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit Rpo5 ...DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase, subunit E / DNA-directed RNA polymerase, subunit F / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit Rpo5 / Transcription factor E / DNA-directed RNA polymerase subunit Rpo3
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsHyun J / Jun S-H / Cho H-S / Murakami KS
Funding support United States, Korea, Republic Of, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteR35 GM131860 United States
Ministry of Education (Korea)NRF-2017M3A9F6029755 Korea, Republic Of
Ministry of Education (Korea)2015R1D1A1A01059097 Korea, Republic Of
Ministry of Education (Korea)NRF-2019M3E5D6063903 Korea, Republic Of
CitationJournal: To Be Published
Title: Thermococcus kodakraensis RNA polymerase in apo form
Authors: Hyun J / Jun S-H / Cho H-S / Murakami KS
History
DepositionJul 3, 2019-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateDec 23, 2020-
Current statusDec 23, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kf4
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9961.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 176 pix.
= 246.4 Å
1.4 Å/pix.
x 176 pix.
= 246.4 Å
1.4 Å/pix.
x 176 pix.
= 246.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.470219 - 0.8160391
Average (Standard dev.)0.001503523 (±0.025279194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 246.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z246.400246.400246.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS176176176
D min/max/mean-0.4700.8160.002

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Supplemental data

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Segmentation: #1

Fileemd_9961_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Tko RNAP-TFE halfmap 1

Fileemd_9961_half_map_1.map
AnnotationTko RNAP-TFE halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Tko RNAP-TFE halfmap 2

Fileemd_9961_half_map_2.map
AnnotationTko RNAP-TFE halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Thermococcus kodakarensis RNA polymerase in complex with transcri...

EntireName: Thermococcus kodakarensis RNA polymerase in complex with transcription factor E
Details: RNA polymerase from euryarchaea (Thermococcus kodakarensis) composed of 11 subunits (Rpo1', Rpo1", Rpo2, Rpo3, Rpo4, Rpo5, Rpo6, Rpo7, Rpo10, Rpo11, Rpo12), and in complex with transcription factor E
Number of Components: 1

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Component #1: protein, Thermococcus kodakarensis RNA polymerase in complex with...

ProteinName: Thermococcus kodakarensis RNA polymerase in complex with transcription factor E
Details: RNA polymerase from euryarchaea (Thermococcus kodakarensis) composed of 11 subunits (Rpo1', Rpo1", Rpo2, Rpo3, Rpo4, Rpo5, Rpo6, Rpo7, Rpo10, Rpo11, Rpo12), and in complex with transcription factor E
Recombinant expression: No
MassTheoretical: 410 kDa
SourceSpecies: Thermococcus kodakarensis KOD1 (archaea)

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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: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 278 K / Humidity: 90 %

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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: 63 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 47000 X (nominal), 100000 X (calibrated) / Cs: 0.002 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1500.0 - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 2698

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 252508
Details: Movie frame data was subjected to motion correction to generate summed micrographs using MotionCor2.
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION
CTF correction: Defocus parameters were calculated from motion-corrected micrographs, using Gctf 1.06. Using the defocus parameters, Cs (0.003, after Cs image corrector tuning) and amplitude contrast ...CTF correction: Defocus parameters were calculated from motion-corrected micrographs, using Gctf 1.06. Using the defocus parameters, Cs (0.003, after Cs image corrector tuning) and amplitude contrast (0.1), CTF phase flipping and amplitude correction was performed during the reconstruction using Relion 2.1.
Resolution: 4 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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