[English] 日本語
Yorodumi
- PDB-3j0k: Orientation of RNA polymerase II within the human VP16-Mediator-p... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3j0k
TitleOrientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly
DescriptorDNA-directed RNA polymerase II largest subunit
DNA-directed RNA polymerase II 140 kDa polypeptide
DNA-directed RNA polymerase II 45 kDa polypeptide
DNA-directed RNA polymerase II 32 kDa polypeptide
DNA-directed RNA polymerases I/II/III 27 kDa polypeptide
and more 7 items
KeywordsTRANSFERASE/TRANSCRIPTION / TRANSFERASE-TRANSCRIPTION complex
Specimen sourceHomo sapiens / human
MethodElectron microscopy (36 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsBernecky, C. / Grob, P. / Ebmeier, C.C. / Nogales, E. / Taatjes, D.J.
CitationPLoS Biol., 2011, 9, e1000603-e1000603

PLoS Biol., 2011, 9, e1000603-e1000603 StrPapers
Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.
Carrie Bernecky / Patricia Grob / Christopher C Ebmeier / Eva Nogales / Dylan J Taatjes

DateDeposition: Oct 4, 2011 / Release: Oct 19, 2011 / Last modification: Oct 26, 2011

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5343
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase II largest subunit
B: DNA-directed RNA polymerase II 140 kDa polypeptide
C: DNA-directed RNA polymerase II 45 kDa polypeptide
D: DNA-directed RNA polymerase II 32 kDa polypeptide
E: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
F: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
G: DNA-directed RNA polymerase II 19 kDa polypeptide
H: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
I: DNA-directed RNA polymerase II subunit 9
J: DNA-directed RNA polymerases I/II/III subunit 10
K: DNA-directed RNA polymerase II 13.6 kDa polypeptide
L: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,20822
Polyers469,59512
Non-polymers61310
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Polypeptide(L) , 12 types, 12 molecules ABCDEFGHIJKL

#1: Polypeptide(L)DNA-directed RNA polymerase II largest subunit


Mass: 163180.906 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138938.062 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

  • DNA-directed RNA polymerase II, core complex (GO: 0005665)

Molecular function

Biological process

#3: Polypeptide(L)DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 30140.277 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.395 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • DNA repair (GO: 0006281)
  • mRNA export from nucleus in response to heat stress (GO: 0031990)
  • nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO: 0000288)
  • positive regulation of translational initiation (GO: 0045948)
  • recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (GO: 0034402)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription initiation from RNA polymerase II promoter (GO: 0006367)
  • transcription, RNA-templated (GO: 0001172)
#5: Polypeptide(L)DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide


Mass: 25117.262 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#6: Polypeptide(L)DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide


Mass: 9675.320 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#7: Polypeptide(L)DNA-directed RNA polymerase II 19 kDa polypeptide


Mass: 19081.186 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • nuclear-transcribed mRNA catabolic process, exonucleolytic (GO: 0000291)
  • positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO: 0060213)
  • positive regulation of translational initiation (GO: 0045948)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription initiation from RNA polymerase II promoter (GO: 0006367)
  • transcription, RNA-templated (GO: 0001172)
#8: Polypeptide(L)DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide


Mass: 16525.500 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#9: Polypeptide(L)DNA-directed RNA polymerase II subunit 9


Mass: 14308.247 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter (GO: 0001193)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription initiation from RNA polymerase II promoter (GO: 0006367)
  • transcription, RNA-templated (GO: 0001172)
  • transcription-coupled nucleotide-excision repair (GO: 0006283)
#10: Polypeptide(L)DNA-directed RNA polymerases I/II/III subunit 10


Mass: 8290.787 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#11: Polypeptide(L)DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.628 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

  • DNA-directed RNA polymerase II, core complex (GO: 0005665)

Molecular function

Biological process

#12: Polypeptide(L)DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide


Mass: 5252.292 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

-
Non-polymers , 2 types, 10 molecules

#13: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg
#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.380 Da / Num. of mol.: 9 / Formula: Zn

-
Details

Sequence detailsTHIS ENTRY WAS MODELED WITH HOMOLOGOUS PROTEIN SEQUENCES FROM SACCHAROMYCES CEREVISIAE.

+
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

-
Sample preparation

Assembly of specimenAggregation state: PARTICLE / Composition: one Mediator complex binds one pol II-TFIIF / Mol wt theo: 1.9 MDa / Number of components: 3
Component

Assembly id: 1 / Ebi cell: HeLa / Ebi organelle: Nucleus / Ebi organism scientific: Homo sapiens / Type: PROTEIN / Ebi expression system: Escherichia coli

IDNameEbi organism commonMutant flagOligomeric detailsSynonym
1core MediatorhumanNO26 subunit complexMediator
2RNA polymerase IIHumanNO12-subunit complexpol II
3TFIIFHumanYESDimerTFIIF
Sample preparationDetails: 20 mM HEPES, 0.10 mM EDTA, 150 mM KCl, 0.02% NP-40, 35% glycerol
pH: 7.9
Specimen supportDetails: thin carbon-coated holey carbon 400 mesh copper grid
VitrificationCryogen name: ETHANE / Temp: 90 K
Method: blot for 2 seconds, dry for 3 seconds before plunging

-
Electron microscopy imaging

EM imagingCamera length: 0 mm
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: side entry / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: Kodak SO-163 film
EM image scansNumber digital images: 106 / Od range: 1 / Quant bit size: 16 / Sampling size: 12.9 microns / Scanner model: OTHER
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Image selectionSoftware name: Situs
EM single particle entitySymmetry type: ASYMMETRIC
3D reconstructionMethod: multi-reference projection matching / Software: Spider / Resolution: 36 A / Resolution method: FSC at 0.5 cut-off / Number of particles: 3146 / CTF correction method: each micrograph / Details: The particles were selected interactively.
Atomic model buildingSoftware name: Situs / Details: the TFIIS chain S was removed before fitting / Ref protocol: rigid body / Ref space: REAL / Target criteria: contour-based Laplacian correlation
Atomic model buildingPDB-ID: 1Y1V
Number of atoms included #LASTProtein: 31127 / Nucleic acid: 0 / Ligand: 10 / Solvent: 0 / Total: 31137

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more