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- PDB-4gwp: Structure of the Mediator Head Module from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 4gwp
TitleStructure of the Mediator Head Module from S. cerevisiae
Components(Mediator of RNA polymerase II transcription subunit ...) x 7
KeywordsTRANSCRIPTION / Binding Sites / Mediator Complex / Models / Molecular / Phosphorylation / Protein Structure / Tertiary / Protein Subunits / RNA Polymerase II / Saccharomyces cerevisiae / Structure-Activity Relationship
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 / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / 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
Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes / Mediator of RNA polymerase II transcription subunit 20 / Mediator complex, subunit Med6, fungi / Mediator complex, subunit Med20 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex ...Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes / Mediator of RNA polymerase II transcription subunit 20 / Mediator complex, subunit Med6, fungi / Mediator complex, subunit Med20 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 4.2 Å
AuthorsRobinson, P.J.J. / Bushnell, D.A. / Trnka, M.J. / Burlingame, A.L. / Kornberg, R.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the Mediator Head module bound to the carboxy-terminal domain of RNA polymerase II.
Authors: Robinson, P.J. / Bushnell, D.A. / Trnka, M.J. / Burlingame, A.L. / Kornberg, R.D.
History
DepositionSep 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mediator of RNA polymerase II transcription subunit 11
B: Mediator of RNA polymerase II transcription subunit 17
C: Mediator of RNA polymerase II transcription subunit 8
D: Mediator of RNA polymerase II transcription subunit 22
E: Mediator of RNA polymerase II transcription subunit 18
F: Mediator of RNA polymerase II transcription subunit 20
G: Mediator of RNA polymerase II transcription subunit 6


Theoretical massNumber of molelcules
Total (without water)241,7927
Polymers241,7927
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.011, 142.011, 305.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Mediator of RNA polymerase II transcription subunit ... , 7 types, 7 molecules ABCDEFG

#1: Protein Mediator of RNA polymerase II transcription subunit 11 / Mediator complex subunit 11


Mass: 13324.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q99278
#2: Protein Mediator of RNA polymerase II transcription subunit 17 / Mediator complex subunit 17 / Suppressor of RNA polymerase B 4


Mass: 78582.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32569
#3: Protein Mediator of RNA polymerase II transcription subunit 8 / Mediator complex subunit 8


Mass: 45930.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38304
#4: Protein Mediator of RNA polymerase II transcription subunit 22 / Mediator complex subunit 22 / Suppressor of RNA polymerase B 6


Mass: 13875.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32570
#5: Protein Mediator of RNA polymerase II transcription subunit 18 / Mediator complex subunit 18 / Suppressor of RNA polymerase B 5


Mass: 34316.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32585
#6: Protein Mediator of RNA polymerase II transcription subunit 20 / Hyper-recombination suppressor protein 2 / Mediator complex subunit 20 / Suppressor of RNA polymerase B 2


Mass: 22918.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P34162
#7: Protein Mediator of RNA polymerase II transcription subunit 6 / Mediator complex subunit 6


Mass: 32844.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38782

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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: 3.71 Å3/Da / Density % sol: 66.88 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 30, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 4.2→122.985 Å / Num. all: 26791 / Num. obs: 26621 / % possible obs: 99.37 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 4.2→4.43 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 4.2→45 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.884 / SU B: 74.271 / SU ML: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.915 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.35709 1341 5 %RANDOM
Rwork0.29038 ---
all0.29366 26754 --
obs0.29366 25254 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 162.713 Å2
Baniso -1Baniso -2Baniso -3
1-5.06 Å22.53 Å20 Å2
2--5.06 Å20 Å2
3----7.59 Å2
Refinement stepCycle: LAST / Resolution: 4.2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9033 0 0 0 9033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199093
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.95612524
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.91951529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74324.877162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.27415693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9161519
X-RAY DIFFRACTIONr_chiral_restr0.0950.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.2→4.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 86 -
Rwork0.371 1656 -
obs--97.05 %

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