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- PDB-4h61: Structure of the Schizosaccharomyces pombe Mediator subunit Med6 -

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Basic information

Entry
Database: PDB / ID: 4h61
TitleStructure of the Schizosaccharomyces pombe Mediator subunit Med6
ComponentsMediator of RNA polymerase II transcription subunit 6
KeywordsTRANSCRIPTION / MEDIATOR COMPLEX / NUCLEUS
Function / homology
Function and homology information


core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / transcription coactivator activity / regulation of transcription by RNA polymerase II
Similarity search - Function
Mediator complex, subunit Med6 / Mediator complex, subunit Med6, fungi / Mediator complex, subunit Med6 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 6
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mediator of RNA polymerase II transcription subunit 6
B: Mediator of RNA polymerase II transcription subunit 6


Theoretical massNumber of molelcules
Total (without water)40,9942
Polymers40,9942
Non-polymers00
Water00
1
A: Mediator of RNA polymerase II transcription subunit 6


Theoretical massNumber of molelcules
Total (without water)20,4971
Polymers20,4971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mediator of RNA polymerase II transcription subunit 6


Theoretical massNumber of molelcules
Total (without water)20,4971
Polymers20,4971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-23 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.950, 125.950, 125.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Mediator of RNA polymerase II transcription subunit 6 / Mediator complex subunit 6 / RNA polymerase II mediator complex protein pmc5


Mass: 20497.107 Da / Num. of mol.: 2 / Fragment: unp reisdues 10-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h / Gene: med6, pmc5, SPAC1002.15c / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9US45

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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: 4.06 Å3/Da / Density % sol: 69.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 400 mM sodium citrate , 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: 0.9189 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9189 Å / Relative weight: 1
ReflectionResolution: 2.7→89.06 Å / Num. all: 18565 / Num. obs: 18565 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 41.4
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 19.3 % / Rmerge(I) obs: 1.0102 / Mean I/σ(I) obs: 0.6 / Num. unique all: 1340 / Rsym value: 1.0102 / % possible all: 100

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→89.06 Å / SU ML: 0.35 / σ(F): 1.99 / Phase error: 26.74 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 928 5 %RANDOM
Rwork0.1812 ---
obs0.183 18562 99.94 %-
all-18565 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→89.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 0 0 2254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062308
X-RAY DIFFRACTIONf_angle_d0.9673123
X-RAY DIFFRACTIONf_dihedral_angle_d14.879867
X-RAY DIFFRACTIONf_chiral_restr0.069339
X-RAY DIFFRACTIONf_plane_restr0.004398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.84240.37111300.3112478X-RAY DIFFRACTION100
2.8424-3.02050.31661320.27632498X-RAY DIFFRACTION100
3.0205-3.25370.28031300.23312474X-RAY DIFFRACTION100
3.2537-3.58110.21911270.17892519X-RAY DIFFRACTION100
3.5811-4.09930.20841400.16132504X-RAY DIFFRACTION100
4.0993-5.16470.18211340.15532521X-RAY DIFFRACTION100
5.1647-89.10850.21931350.18482640X-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)
12.66320.99740.36072.139-0.60934.17080.20780.1838-0.96070.3175-0.1433-0.13210.7096-0.2347-0.00010.8093-0.0637-0.00070.9951-0.14641.260737.306191.852874.3643
21.4935-0.6690.00120.50090.12730.08251.21540.64460.78240.1899-1.2089-0.026-0.8140.1907-0.01640.9713-0.1019-0.14661.5358-0.20511.480819.3317100.851464.0153
32.00560.81210.46264.55430.01212.61920.0012-0.71120.15590.59210.0889-0.97850.26740.12050.00040.8084-0.0272-0.19811.3437-0.18861.37353.377984.080960.6498
42.83640.9923-0.8370.8056-0.71220.62970.67510.45191.093-1.02290.38180.04760.3542-0.02580.53791.2382-0.2505-0.12771.6697-0.40651.307122.956693.994855.8623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 8:118)
2X-RAY DIFFRACTION2(chain A and resseq 119:144)
3X-RAY DIFFRACTION3(chain B and resseq 8:118)
4X-RAY DIFFRACTION4(chain B and resseq 119:147)

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