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- PDB-4h62: Structure of the Saccharomyces cerevisiae Mediator subcomplex Med... -

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Basic information

Entry
Database: PDB / ID: 4h62
TitleStructure of the Saccharomyces cerevisiae Mediator subcomplex Med17C/Med11C/Med22C
Components
  • Mediator of RNA polymerase II transcription subunit 11
  • Mediator of RNA polymerase II transcription subunit 17
  • Mediator of RNA polymerase II transcription subunit 22
KeywordsTRANSCRIPTION / MEDIATOR COMPLEX / NUCLEUS
Function / homology
Function and homology information


RNA polymerase II complex recruiting activity / TFIIH-class transcription factor complex binding / core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II complex recruiting activity / TFIIH-class transcription factor complex binding / core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / cellular response to heat / 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
Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes / Mediator complex, subunit Med17 / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator complex 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 11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsLariviere, L. / Plaschka, C. / Seizl, M. / Wenzeck, L. / Kurth, F. / Cramer, P.
CitationJournal: Nature / Year: 2012
Title: Structure of the Mediator head module.
Authors: Lariviere, L. / Plaschka, C. / Seizl, M. / Wenzeck, L. / Kurth, F. / Cramer, P.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Mediator of RNA polymerase II transcription subunit 11
V: Mediator of RNA polymerase II transcription subunit 22
Q: Mediator of RNA polymerase II transcription subunit 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4944
Polymers44,2993
Non-polymers1951
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-27 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.230, 261.230, 47.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 4341.593 Da / Num. of mol.: 1 / Fragment: C-terminal region (Unp residues 84-115)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: MED11, YM9718.11C, YMR112C / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pRARE / References: UniProt: Q99278
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 22 / Mediator complex subunit 22 / Suppressor of RNA polymerase B 6


Mass: 3404.732 Da / Num. of mol.: 1 / Fragment: C-terminal region (Unp residues 96-121)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: MED22, SRB6, YBR1721, YBR253W / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pRARE / References: UniProt: P32570
#3: Protein Mediator of RNA polymerase II transcription subunit 17 / Mediator complex subunit 17 / Suppressor of RNA polymerase B 4


Mass: 36552.348 Da / Num. of mol.: 1 / Fragment: C-terminal region (Unp residues 377-687)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: MED17, SRB4, YER022W / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pRARE / References: UniProt: P32569
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
Has protein modificationY

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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: 3.54 Å3/Da / Density % sol: 65.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, 4 M ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97972 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 3→130.615 Å / Num. all: 24338 / Num. obs: 24338 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 16.46
Reflection shellResolution: 3→3.08 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.6922 / Mean I/σ(I) obs: 0.56 / Rsym value: 0.6922 / % possible all: 100

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Processing

Software
NameVersionClassification
RemDAqdata collection
SHELXCDphasing
SHELXEmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3→65.308 Å / SU ML: 0.41 / σ(F): 1.23 / Phase error: 31.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 621 4.99 %
Rwork0.2043 --
obs0.2056 24328 99.88 %
all-24338 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→65.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 12 0 2556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072586
X-RAY DIFFRACTIONf_angle_d1.2183477
X-RAY DIFFRACTIONf_dihedral_angle_d17.4391015
X-RAY DIFFRACTIONf_chiral_restr0.083416
X-RAY DIFFRACTIONf_plane_restr0.005434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.12030.38871390.35862554X-RAY DIFFRACTION100
3.1203-3.26230.40651200.33082567X-RAY DIFFRACTION100
3.2623-3.43420.33751390.28682590X-RAY DIFFRACTION100
3.4342-3.64940.26141350.24232568X-RAY DIFFRACTION100
3.6494-3.93110.24371340.20572548X-RAY DIFFRACTION100
3.9311-4.32670.25161360.18942586X-RAY DIFFRACTION100
4.3267-4.95260.18061340.15312563X-RAY DIFFRACTION100
4.9526-6.23890.22231380.20622568X-RAY DIFFRACTION100
6.2389-65.32290.20191390.19342570X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6819-1.5348-0.56635.16482.00750.7862-0.36440.09740.01470.64211.1533-0.46670.6065-1.80530.85231.6481-0.4746-0.25342.12410.57491.189832.2847112.654795.3126
21.75620.65170.89579.11257.3876.06490.0963-1.2561-0.1580.5946-1.28981.8344-0.3833-1.373-1.87711.2972-0.06770.13021.13740.09810.791641.6547123.708598.3504
35.90092.59180.34093.1549-0.13534.465-0.03850.3658-0.74730.0679-0.0852-0.1740.2578-0.0592-2.78251.04190.0577-0.13530.85530.04641.140141.2822112.237784.1853
42.12090.3001-0.68022.8806-0.72023.4520.2571-0.3632-0.4130.3328-0.075-0.5063-0.42610.0157-0.00011.20480.0098-0.09331.01770.12790.916956.2513142.685888.7657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN K AND RESID 93:111 )K93 - 111
2X-RAY DIFFRACTION2( CHAIN V AND RESID 100:121 )V100 - 121
3X-RAY DIFFRACTION3( CHAIN Q AND ( RESID 383:541 OR RESID 594:611 ) )Q383 - 541
4X-RAY DIFFRACTION3( CHAIN Q AND ( RESID 383:541 OR RESID 594:611 ) )Q594 - 611
5X-RAY DIFFRACTION4( CHAIN Q AND ( RESID 542:580 OR RESID 612:684 ) )Q542 - 580
6X-RAY DIFFRACTION4( CHAIN Q AND ( RESID 542:580 OR RESID 612:684 ) )Q612 - 684

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