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Yorodumi- PDB-3j1o: Cryo-EM map of a yeast minimal preinitiation complex interacting ... -
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-Basic information
Entry | Database: PDB / ID: 3j1o | ||||||
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Title | Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module | ||||||
Components | (Mediator of RNA polymerase II transcription subunit ...) x 7 | ||||||
Keywords | TRANSCRIPTION / RNA polymerase II / mediator head module / preinitiation complex | ||||||
Function / homology | Function and homology information RNA polymerase II complex recruiting activity / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / mediator complex / termination of RNA polymerase II transcription / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding ...RNA polymerase II complex recruiting activity / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / mediator complex / termination of RNA polymerase II transcription / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to nutrient levels / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / transcription corepressor activity / protein-macromolecule adaptor activity / cellular response to heat / DNA-binding transcription factor binding / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16 Å | ||||||
Authors | Asturias, F.J. / Imasaki, T. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Interaction of the mediator head module with RNA polymerase II. Authors: Gang Cai / Yuriy L Chaban / Tsuyoshi Imasaki / Julio A Kovacs / Guillermo Calero / Pawel A Penczek / Yuichiro Takagi / Francisco J Asturias / Abstract: Mediator, a large (21 polypeptides, MW ∼1 MDa) complex conserved throughout eukaryotes, plays an essential role in control of gene expression by conveying regulatory signals that influence the ...Mediator, a large (21 polypeptides, MW ∼1 MDa) complex conserved throughout eukaryotes, plays an essential role in control of gene expression by conveying regulatory signals that influence the activity of the preinitiation complex. However, the precise mode of interaction between Mediator and RNA polymerase II (RNAPII), and the mechanism of regulation by Mediator remain elusive. We used cryo-electron microscopy and reconstituted in vitro transcription assays to characterize a transcriptionally-active complex including the Mediator Head module and components of a minimum preinitiation complex (RNAPII, TFIIF, TFIIB, TBP, and promoter DNA). Our results reveal how the Head interacts with RNAPII, affecting its conformation and function. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 3j1o.cif.gz | 324.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j1o.ent.gz | 237.7 KB | Display | PDB format |
PDBx/mmJSON format | 3j1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j1o_validation.pdf.gz | 733.1 KB | Display | wwPDB validaton report |
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Full document | 3j1o_full_validation.pdf.gz | 752.5 KB | Display | |
Data in XML | 3j1o_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 3j1o_validation.cif.gz | 48.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/3j1o ftp://data.pdbj.org/pub/pdb/validation_reports/j1/3j1o | HTTPS FTP |
-Related structure data
Related structure data | 5407MC 3j1nC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Mediator of RNA polymerase II transcription subunit ... , 7 types, 7 molecules HIJKLMN
#1: Protein | Mass: 15100.063 Da / Num. of mol.: 1 / Mutation: T16G, M17S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MED11, YMR112C, YM9718.11C / Plasmid: pBakPAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0D3YMY9, UniProt: Q99278*PLUS |
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#2: Protein | Mass: 54893.527 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SRB4, MED17, YER022W / Plasmid: pBakPAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32569 |
#3: Protein | Mass: 25297.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MED8, YBR193C, YBR1403 / Plasmid: pBakPAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38304 |
#4: Protein | Mass: 13875.731 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SRB6, MED22, YBR253W, YBR1721 / Plasmid: pBakPAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32570 |
#5: Protein | Mass: 30659.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SRB5, MED18, YGR104C / Plasmid: pBakPAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32585 |
#6: Protein | Mass: 22918.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SRB2, HRS2, MED20, YHR041C / Plasmid: pBakPAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P34162 |
#7: Protein/peptide | Mass: 2949.360 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MED6, MTR32, YHR058C / Plasmid: pBakPAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38782 |
-Details
Sequence details | THE ARRANGEMENT OF RESIDUES 617-668 OF CHAIN I IS UNCLEAR. THESE RESIDUES HAVE BEEN DEFINED AS UNK ...THE ARRANGEMEN |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.9 MDa / Experimental value: NO | ||||||||||||||||||||
Buffer solution | Name: 25 mM KCl, 25 mM Tris-HCl, 10 mM DTT / pH: 8 / Details: 25 mM KCl, 25 mM Tris-HCl, 10 mM DTT | ||||||||||||||||||||
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 25mM KCl, 25mM Tris-HCl, 10mM DTT | ||||||||||||||||||||
Specimen support | Details: 400 mesh Cu/Rh grids, coated with a perforated carbon film and glow discharged in the presence of amylamine | ||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 77 K / Humidity: 95 % Details: Blot for approximately 2 seconds before plunging into liquid ethane. Method: Blot for ~2 sec before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jul 30, 2008 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3800 nm / Nominal defocus min: 800 nm / Cs: 2 mm Astigmatism: Objective lens astigmatisma was corrected at 125,000X magnification Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Temperature: 115 K / Temperature (max): 120 K / Temperature (min): 77 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Each CCD frame | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Method: projection matching / Resolution: 16 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 51000 / Symmetry type: POINT | ||||||||||||||||
Atomic model building |
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Atomic model building | 3D fitting-ID: 1 / Accession code: 3RJ1 / Initial refinement model-ID: 1 / PDB-ID: 3RJ1 / Source name: PDB / Type: experimental model
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Refinement step | Cycle: LAST
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