[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
Descriptor(DNA-directed RNA polymerase II ...) x 7
(DNA-directed RNA polymerases I/II/III ...) x 5
KeywordsTRANSFERASE/TRANSCRIPTION / TRANSFERASE-TRANSCRIPTION complex
Specimen sourceHomo sapiens / human
MethodElectron microscopy (36 Å resolution / Particle / Single particle)
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 4, 2011 / Release: Oct 19, 2011
RevisionDateData content typeGroupProviderType
1.0Oct 19, 2011Structure modelrepositoryInitial release
1.1Oct 26, 2011Structure modelStructure summary

-
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)470,20522
Polyers469,59212
Non-polymers61310
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
DNA-directed RNA polymerase II ... , 7 types, 7 molecules ABCDGIK

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


Mass: 163180.016 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: 138937.297 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

Cellular component

Molecular function

Biological process

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


Mass: 30140.059 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: 25451.191 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)
#7: Polypeptide(L)DNA-directed RNA polymerase II 19 kDa polypeptide


Mass: 19081.053 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)
#9: Polypeptide(L)DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 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)
  • mRNA cleavage (GO: 0006379)
  • 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)
#11: Polypeptide(L)DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 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

-
DNA-directed RNA polymerases I, II, and III ... , 4 types, 4 molecules EFHL

#5: Polypeptide(L)DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide


Mass: 25117.094 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: 9675.230 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)
#8: Polypeptide(L)DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide


Mass: 16525.363 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)
#12: Polypeptide(L)DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide


Mass: 5252.261 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: EC: 2.7.7.6

-
Polypeptide(L) , 1 types, 1 molecules J

#10: Polypeptide(L)DNA-directed RNA polymerases I/II/III subunit 10


Mass: 8290.732 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)

-
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: 65.409 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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

Component
IDNameTypeDetailsParent IDSynonym
1RNA polymerase II VP16-Mediator-pol II-TFIIF assemblyCOMPLEXone Mediator complex binds one pol II-TFIIF0
2core Mediator26 subunit complex1Mediator
3RNA polymerase II12-subunit complex1pol II
4TFIIFDimer1TFIIF
Molecular weightValue: 1.9 deg. / Units: MEGADALTONS / Experimental value: NO
Buffer solutionDetails: 20 mM HEPES, 0.10 mM EDTA, 150 mM KCl, 0.02% NP-40, 35% glycerol
pH: 7.9
SpecimenDetails: 20 mM HEPES, 0.10 mM EDTA, 150 mM KCl, 0.02% NP-40, 35% glycerol
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM stainingType: NEGATIVE
Details: grids with adsorbed protein washed 3x with buffer containing 5% trehalose, 20 mM HEPES, 100 mM KCl, and 0.10 mM EDTA, then subjected to cryo-negative staining in a saturated solution (1.2M) of ammonium molybdate (pH 7.5)
Material: ammonium molybdate
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

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 29000 / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: side entry / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansSampling size: 12.9 microns / Number digital images: 106 / Od range: 1 / Quant bit size: 16 / Scanner model: OTHER
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1SitusMODEL FITTING
2SPIDERRECONSTRUCTION
CTF correctionDetails: each micrograph
SymmetryPoint symmetry: C1
3D reconstructionMethod: multi-reference projection matching / Resolution: 36 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 3146 / Details: The particles were selected interactively. / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body DETAILS--the TFIIS chain S was removed before fitting
Ref protocol: RIGID BODY FIT / 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

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
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

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