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- PDB-2hzs: Structure of the Mediator head submodule Med8C/18/20 -

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Basic information

Entry
Database: PDB / ID: 2hzs
TitleStructure of the Mediator head submodule Med8C/18/20
Components
  • RNA polymerase II mediator complex subunit 18
  • RNA polymerase II mediator complex subunit 20
  • RNA polymerase II mediator complex subunit 8
KeywordsTRANSCRIPTION / beta barrel / channel / helix
Function / homology
Function and homology information


transcription open complex formation at RNA polymerase II promoter / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / mediator complex / termination of RNA polymerase II transcription / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly ...transcription open complex formation at RNA polymerase II promoter / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / mediator complex / termination of RNA polymerase II transcription / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / transcription corepressor activity / cellular response to heat / protein-macromolecule adaptor activity / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / 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
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 Med8, fungi/metazoa / Mediator of RNA polymerase II transcription complex subunit 8 ...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 Med8, fungi/metazoa / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex, subunit Med18 / Med18 protein / TATA-Binding Protein / Single Sheet / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
I: RNA polymerase II mediator complex subunit 8
J: RNA polymerase II mediator complex subunit 8
K: RNA polymerase II mediator complex subunit 8
L: RNA polymerase II mediator complex subunit 8


Theoretical massNumber of molelcules
Total (without water)240,87112
Polymers240,87112
Non-polymers00
Water1,53185
1
A: RNA polymerase II mediator complex subunit 20
B: RNA polymerase II mediator complex subunit 18
I: RNA polymerase II mediator complex subunit 8


Theoretical massNumber of molelcules
Total (without water)60,2183
Polymers60,2183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA polymerase II mediator complex subunit 20
D: RNA polymerase II mediator complex subunit 18
J: RNA polymerase II mediator complex subunit 8


Theoretical massNumber of molelcules
Total (without water)60,2183
Polymers60,2183
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-44 kcal/mol
Surface area20050 Å2
MethodPISA
3
E: RNA polymerase II mediator complex subunit 20
F: RNA polymerase II mediator complex subunit 18
K: RNA polymerase II mediator complex subunit 8


Theoretical massNumber of molelcules
Total (without water)60,2183
Polymers60,2183
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-43 kcal/mol
Surface area20670 Å2
MethodPISA
4
G: RNA polymerase II mediator complex subunit 20
H: RNA polymerase II mediator complex subunit 18
L: RNA polymerase II mediator complex subunit 8


Theoretical massNumber of molelcules
Total (without water)60,2183
Polymers60,2183
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA polymerase II mediator complex subunit 20
F: RNA polymerase II mediator complex subunit 18
K: RNA polymerase II mediator complex subunit 8

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
G: RNA polymerase II mediator complex subunit 20
H: RNA polymerase II mediator complex subunit 18
I: RNA polymerase II mediator complex subunit 8
J: RNA polymerase II mediator complex subunit 8
L: RNA polymerase II mediator complex subunit 8


Theoretical massNumber of molelcules
Total (without water)240,87112
Polymers240,87112
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation2_646-x+1,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area31710 Å2
ΔGint-234 kcal/mol
Surface area74490 Å2
MethodPISA
6
G: RNA polymerase II mediator complex subunit 20
H: RNA polymerase II mediator complex subunit 18
L: RNA polymerase II mediator complex subunit 8

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
I: RNA polymerase II mediator complex subunit 8
J: RNA polymerase II mediator complex subunit 8
K: RNA polymerase II mediator complex subunit 8


Theoretical massNumber of molelcules
Total (without water)240,87112
Polymers240,87112
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation2_656-x+1,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area30840 Å2
ΔGint-211 kcal/mol
Surface area75360 Å2
MethodPISA
7
A: RNA polymerase II mediator complex subunit 20
B: 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
I: RNA polymerase II mediator complex subunit 8
K: RNA polymerase II mediator complex subunit 8
L: RNA polymerase II mediator complex subunit 8


Theoretical massNumber of molelcules
Total (without water)180,6549
Polymers180,6549
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22350 Å2
ΔGint-161 kcal/mol
Surface area58190 Å2
MethodPISA
8
A: RNA polymerase II mediator complex subunit 20
B: RNA polymerase II mediator complex subunit 18
G: RNA polymerase II mediator complex subunit 20
H: RNA polymerase II mediator complex subunit 18
I: RNA polymerase II mediator complex subunit 8
L: RNA polymerase II mediator complex subunit 8


Theoretical massNumber of molelcules
Total (without water)120,4366
Polymers120,4366
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-110 kcal/mol
Surface area40060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.365, 115.762, 129.159
Angle α, β, γ (deg.)90.00, 98.49, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a heterotrimer formed by one molecule 1, one molecule 2 and one molecule 3. Four biological assemblies are present in the asymetric unit: A/B/I, C/D/J, E/F/K, G/H/L.

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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: 22786.869 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: 34213.391 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: Protein/peptide
RNA polymerase II mediator complex subunit 8 / RNA polymerase II transcriptional regulation mediator 8


Mass: 3217.593 Da / Num. of mol.: 4 / Fragment: C-terminal domain, residues 189-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MED8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P38304
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM sodium acetate, 0.6 M sodium fluoride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 61548 / Num. obs: 61548 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.075 / Net I/σ(I): 19.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.463 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HZM

2hzm


Resolution: 2.7→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 3047 RANDOM
Rwork0.236 --
all-61548 -
obs-61548 -
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14001 0 0 85 14086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.261
X-RAY DIFFRACTIONc_bond_d0.008

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