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- PDB-1zp2: Structure of the Mediator subunit cyclin C -

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Basic information

Entry
Database: PDB / ID: 1zp2
TitleStructure of the Mediator subunit cyclin C
ComponentsRNA polymerase II holoenzyme cyclin-like subunit
KeywordsTranscription/Cell Cycle / cyclin repeat domains / Transcription-Cell Cycle COMPLEX
Function / homology
Function and homology information


mediator complex / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of transcription initiation by RNA polymerase II / transcription coactivator activity / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Cyclin C/cyclin-like subunit Ssn8 / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase II holoenzyme cyclin-like subunit
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsHoeppner, S. / Baumli, S. / Cramer, P.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of the Mediator Subunit Cyclin C and its Implications for CDK8 Function.
Authors: Hoeppner, S. / Baumli, S. / Cramer, P.
History
DepositionMay 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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: RNA polymerase II holoenzyme cyclin-like subunit


Theoretical massNumber of molelcules
Total (without water)27,1001
Polymers27,1001
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA polymerase II holoenzyme cyclin-like subunit

A: RNA polymerase II holoenzyme cyclin-like subunit


Theoretical massNumber of molelcules
Total (without water)54,2012
Polymers54,2012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area3460 Å2
ΔGint-24 kcal/mol
Surface area23180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.700, 91.700, 91.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a monomer

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Components

#1: Protein RNA polymerase II holoenzyme cyclin-like subunit / / Suppressor of RNA polymerase B srb11


Mass: 27100.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: srb11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: O94503

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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: 4.4 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium acetate, imidazole, PEG 400, Tris, sodium chloride, glycerol, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11.0725
SYNCHROTRONSLS X06SA20.97977, 0.98004, 0.94927
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 16, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.07251
20.979771
30.980041
40.949271
ReflectionResolution: 3→20 Å / Num. all: 9161 / Num. obs: 9161 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.16 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2882 488 RANDOM
Rwork0.2443 --
all0.2904 9161 -
obs0.2904 9131 -
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 0 0 1823
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.30123
X-RAY DIFFRACTIONc_bond_d0.008243

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