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- PDB-3c0t: Structure of the Schizosaccharomyces pombe Mediator subcomplex Me... -

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Basic information

Entry
Database: PDB / ID: 3c0t
TitleStructure of the Schizosaccharomyces pombe Mediator subcomplex Med8C/18
Components
  • Mediator of RNA polymerase II transcription subunit 18
  • Mediator of RNA polymerase II transcription subunit 8
KeywordsTRANSCRIPTION / BETA BARREL / CHANNEL / PROTEIN-PROTEIN COMPLEX / Activator / Nucleus / Transcription regulation
Function / homology
Function and homology information


core mediator complex / mediator complex / positive regulation of transcription initiation by RNA polymerase II / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / Mediator complex, subunit Med8, fungi/metazoa / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex, subunit Med18 / Med18 protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 8
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLariviere, L. / Seizl, M. / van Wageningen, S. / Roether, S. / van de Pasch, L. / Feldmann, H. / Straesser, K. / Hahn, S. / Holstege, C.P. / Cramer, P.
CitationJournal: Genes Dev. / Year: 2008
Title: Structure-system correlation identifies a gene regulatory Mediator submodule
Authors: Lariviere, L. / Seizl, M. / van Wageningen, S. / Rother, S. / van de Pasch, L. / Feldmann, H. / Strasser, K. / Hahn, S. / Holstege, F.C.P. / Cramer, P.
History
DepositionJan 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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 18
B: Mediator of RNA polymerase II transcription subunit 8


Theoretical massNumber of molelcules
Total (without water)27,9162
Polymers27,9162
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-12.8 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.016, 111.016, 68.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Mediator of RNA polymerase II transcription subunit 18 / Mediator complex subunit 18 / Cell separation protein sep11 / RNA polymerase II mediator complex protein pmc6


Mass: 24056.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O14198
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 8 / Mediator complex subunit 8 / Cell separation protein sep15


Mass: 3859.357 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP Residues 180-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: med8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O94646
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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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: 4.37 Å3/Da / Density % sol: 71.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris pH 8.5, 2M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2006
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 19282 / Num. obs: 19282 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Rsym value: 0.084 / Net I/σ(I): 21.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 2806 / Rsym value: 0.379 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The starting model is the structure of Med18 alone, which has not been deposited.

Resolution: 2.4→20 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2314 937 RANDOM
Rwork0.211 --
all-19282 -
obs-19282 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 0 62 1884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.293
X-RAY DIFFRACTIONc_bond_d0.006

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