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- PDB-2xnf: The Mediator Med25 activator interaction domain: Structure and co... -

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Basic information

Entry
Database: PDB / ID: 2xnf
TitleThe Mediator Med25 activator interaction domain: Structure and cooperative binding of VP16 subdomains
ComponentsMEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 25
KeywordsTRANSCRIPTION / ACTIVATED TRANSCRIPTION / MEDIATOR
Function / homology
Function and homology information


positive regulation of mediator complex assembly / core mediator complex / mediator complex / nuclear retinoic acid receptor binding / Generic Transcription Pathway / positive regulation of chromatin binding / positive regulation of transcription initiation by RNA polymerase II / nuclear retinoid X receptor binding / negative regulation of fibroblast proliferation / RNA polymerase II preinitiation complex assembly ...positive regulation of mediator complex assembly / core mediator complex / mediator complex / nuclear retinoic acid receptor binding / Generic Transcription Pathway / positive regulation of chromatin binding / positive regulation of transcription initiation by RNA polymerase II / nuclear retinoid X receptor binding / negative regulation of fibroblast proliferation / RNA polymerase II preinitiation complex assembly / positive regulation of transcription elongation by RNA polymerase II / transcription coactivator binding / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / transcription regulator complex / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Mediator complex subunit 25, ACID domain / Ku70; Chain: A; Domain 2 / Mediator complex, subunit Med25, PTOV domain / Mediator complex, subunit Med25, synapsin 1 / Mediator of RNA polymerase II transcription subunit 25, von Willebrand factor type A domain / Mediator complex subunit 25, PTOV domain superfamily / Mediator complex subunit 25 PTOV activation and synapsin 2 / Mediator complex subunit 25 synapsin 1 / Mediator complex subunit 25 von Willebrand factor type A / von Willebrand factor A-like domain superfamily ...Mediator complex subunit 25, ACID domain / Ku70; Chain: A; Domain 2 / Mediator complex, subunit Med25, PTOV domain / Mediator complex, subunit Med25, synapsin 1 / Mediator of RNA polymerase II transcription subunit 25, von Willebrand factor type A domain / Mediator complex subunit 25, PTOV domain superfamily / Mediator complex subunit 25 PTOV activation and synapsin 2 / Mediator complex subunit 25 synapsin 1 / Mediator complex subunit 25 von Willebrand factor type A / von Willebrand factor A-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 25
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CYANA
AuthorsVojnic, E. / Mourao, A. / Seizl, M. / Simon, B. / Wenzeck, L. / Lariviere, L. / Baumli, S. / Meisterernst, M. / Sattler, M. / Cramer, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure and Vp16 Binding of the Mediator Med25 Activator Interaction Domain.
Authors: Vojnic, E. / Mourao, A. / Seizl, M. / Simon, B. / Wenzeck, L. / Lariviere, L. / Baumli, S. / Baumgart, K. / Meisterernst, M. / Sattler, M. / Cramer, P.
History
DepositionAug 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 25


Theoretical massNumber of molelcules
Total (without water)18,2841
Polymers18,2841
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100ENERGY
RepresentativeModel #1

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Components

#1: Protein MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 25 / MEDIATOR COMPLEX SUBUNIT 25 / ACTIVATOR-RECRUITED COFACTOR 92 KDA COMPONENT / ARC92 / ACTIVATOR ...MEDIATOR COMPLEX SUBUNIT 25 / ACTIVATOR-RECRUITED COFACTOR 92 KDA COMPONENT / ARC92 / ACTIVATOR INTERACTION DOMAIN-CONTAINING PROTEIN 1 / P78 / MED25


Mass: 18284.301 Da / Num. of mol.: 1 / Fragment: MED25 ACID DOMAIN, RESIDUES 394-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q71SY5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
221HSQC
331HNCA
441HN(CA)CB
551CBCA(CO)NH
661(H)CCH-TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING MULTIDIMENSIONAL NMR SPECTROSCOPY ON 13C, 15N-LABELED MED25 ACID DOMAIN

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Sample preparation

DetailsContents: 90%WATER/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 6.5 1.0 atm295.0 K
2100 mM6.5 1.0 atm295.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance9001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE, SIMONSON,WARRENrefinement
NMRVIEWstructure solution
RefinementMethod: CYANA / Software ordinal: 1 / Details: WATER-REFINED
NMR ensembleConformer selection criteria: ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 10

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