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- PDB-1ykh: Structure of the mediator MED7/MED21 (Med7/Srb7) subcomplex -

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Basic information

Entry
Database: PDB / ID: 1ykh
TitleStructure of the mediator MED7/MED21 (Med7/Srb7) subcomplex
Components
  • RNA polymerase II holoenzyme component SRB7
  • RNA polymerase II mediator complex protein MED7
KeywordsGENE REGULATION
Function / homology
Function and homology information


core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of transcription by RNA polymerase II ...core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / 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
Helix Hairpins - #200 / Mediator complex, subunit Med21 / Mediator complex, subunit Med21 / Mediator complex, subunit Med7 superfmaily / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / MED7 protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix Hairpins ...Helix Hairpins - #200 / Mediator complex, subunit Med21 / Mediator complex, subunit Med21 / Mediator complex, subunit Med7 superfmaily / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / MED7 protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsBaumli, S. / Hoeppner, S. / Cramer, P.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer.
Authors: Baumli, S. / Hoeppner, S. / Cramer, P.
History
DepositionJan 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II mediator complex protein MED7
B: RNA polymerase II holoenzyme component SRB7


Theoretical massNumber of molelcules
Total (without water)28,2802
Polymers28,2802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-37 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.690, 85.690, 182.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein RNA polymerase II mediator complex protein MED7 / RNA polymerase II transcriptional regulation mediator 7


Mass: 12964.011 Da / Num. of mol.: 1 / Fragment: residues 102-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08278
#2: Protein RNA polymerase II holoenzyme component SRB7 / MED21 / RNAPII complex component SRB7 / Suppressor of RNA polymerase B SRB7


Mass: 15315.521 Da / Num. of mol.: 1 / Mutation: L5M, L119M, L125M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P47822

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.4 Å3/Da / Density % sol: 77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, sodium acetate, b-mercaptoethanol, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 3, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 14381 / Num. obs: 14180 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.11 Å / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.289 709 RANDOM
Rwork0.257 --
all-14276 -
obs-14129 -
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 0 0 1736
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.164
X-RAY DIFFRACTIONc_bond_d0.008

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