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- PDB-2hzm: Structure of the Mediator head subcomplex Med18/20 -

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Basic information

Entry
Database: PDB / ID: 2hzm
TitleStructure of the Mediator head subcomplex Med18/20
Components
  • RNA polymerase II mediator complex subunit 18
  • RNA polymerase II mediator complex subunit 20
KeywordsTRANSCRIPTION / beta barrel / channel
Function / homology
Function and homology information


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 preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II ...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 preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / transcription coactivator activity / protein domain specific binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
q64v53_bacfr protein fold - #20 / TATA-Binding Protein - #180 / q64v53_bacfr protein fold / Mediator of RNA polymerase II transcription subunit 20 / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / Mediator complex, subunit Med20 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex, subunit Med18 / Med18 protein ...q64v53_bacfr protein fold - #20 / TATA-Binding Protein - #180 / q64v53_bacfr protein fold / Mediator of RNA polymerase II transcription subunit 20 / Hypothetical Protein Pfu-838710-001 / Hypothetical Protein Pfu-838710-001 / Mediator complex, subunit Med20 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex, subunit Med18 / Med18 protein / TATA-Binding Protein / Single Sheet / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 20
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLariviere, L. / Geiger, S. / Hoeppner, S. / Rother, S. / Straesser, K. / Cramer, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20.
Authors: Lariviere, L. / Geiger, S. / Hoeppner, S. / Rother, S. / Strasser, K. / Cramer, P.
History
DepositionAug 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II mediator complex subunit 20
B: RNA polymerase II mediator complex subunit 18
C: RNA polymerase II mediator complex subunit 20
D: RNA polymerase II mediator complex subunit 18
E: RNA polymerase II mediator complex subunit 20
F: RNA polymerase II mediator complex subunit 18
G: RNA polymerase II mediator complex subunit 20
H: RNA polymerase II mediator complex subunit 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,3919
Polymers234,2968
Non-polymers951
Water4,125229
1
A: RNA polymerase II mediator complex subunit 20
B: RNA polymerase II mediator complex subunit 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6693
Polymers58,5742
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-31 kcal/mol
Surface area20450 Å2
MethodPISA
2
C: RNA polymerase II mediator complex subunit 20
D: RNA polymerase II mediator complex subunit 18


Theoretical massNumber of molelcules
Total (without water)58,5742
Polymers58,5742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-23 kcal/mol
Surface area20040 Å2
MethodPISA
3
E: RNA polymerase II mediator complex subunit 20
F: RNA polymerase II mediator complex subunit 18


Theoretical massNumber of molelcules
Total (without water)58,5742
Polymers58,5742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-21 kcal/mol
Surface area20220 Å2
MethodPISA
4
G: RNA polymerase II mediator complex subunit 20
H: RNA polymerase II mediator complex subunit 18


Theoretical massNumber of molelcules
Total (without water)58,5742
Polymers58,5742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-22 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.903, 129.352, 241.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a heterodimer formed by one molecule 1 and one molecule 2. Four biological assemblies are present in the asymetric unit.

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Components

#1: Protein
RNA polymerase II mediator complex subunit 20 / Suppressor of RNA polymerase B 2 / Hyper-recombination suppressor protein 2


Mass: 23076.225 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SRB2, HRS2, MED20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P34162
#2: Protein
RNA polymerase II mediator complex subunit 18 / Suppressor of RNA polymerase B 5


Mass: 35497.766 Da / Num. of mol.: 4 / Fragment: residues 2-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SRB5, MED18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P32585
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, 1.8 M Na/K phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 89181 / Num. obs: 89181 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Rsym value: 0.073 / Net I/σ(I): 25.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.375 / % possible all: 95.1

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 4276 RANDOM
Rwork0.228 --
all0.228 89181 -
obs0.228 89181 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13353 0 5 229 13587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.371
X-RAY DIFFRACTIONc_bond_d0.008
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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