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- PDB-2ky6: Structure of ARC92VBD/MED25ACID -

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Basic information

Entry
Database: PDB / ID: 2ky6
TitleStructure of ARC92VBD/MED25ACID
ComponentsMediator of RNA polymerase II transcription subunit 25
KeywordsTRANSCRIPTION REGULATOR / Mediator / ARC / VP16 binding domain / ACID
Function / homology
Function and homology information


positive regulation of mediator complex assembly / core mediator complex / nuclear retinoic acid receptor binding / mediator complex / Generic Transcription Pathway / positive regulation of chromatin binding / RSV-host interactions / positive regulation of transcription initiation by RNA polymerase II / nuclear retinoid X receptor binding / negative regulation of fibroblast proliferation ...positive regulation of mediator complex assembly / core mediator complex / nuclear retinoic acid receptor binding / mediator complex / Generic Transcription Pathway / positive regulation of chromatin binding / RSV-host interactions / 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 / PPARA activates gene expression / transcription coactivator binding / 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 / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsMilbradt, A.G. / Sun, Z.J. / Selenko, P. / Takeuchi, K. / Naar, A.M. / Wagner, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure of the VP16 transactivator target in the Mediator.
Authors: Milbradt, A.G. / Kulkarni, M. / Yi, T. / Takeuchi, K. / Sun, Z.Y. / Luna, R.E. / Selenko, P. / Naar, A.M. / Wagner, G.
History
DepositionMay 14, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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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 25


Theoretical massNumber of molelcules
Total (without water)18,9791
Polymers18,9791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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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


Mass: 18979.033 Da / Num. of mol.: 1
Fragment: VP16-binding-domain (VBD) Activator-interacting domain (ACID) (UNP Residues 391-553)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: His-GB1-TEV-tag / Gene: MED25, ACID1, ARC92, PTOV2, TCBAP0758 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71SY5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution NMR structure of Activator-recruited cofactor 92 kDa component
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1322D 1H-1H NOESY
1413D 1H-15N NOESY
1533D 1H-13C NOESY
1643D HNCO
1743D HNCA
1843D HN(CO)CA
1943D HN(CA)CB
11033D (H)CCH-TOCSY
11132D 1H-13C HSQC
11254D HMQCNOESYHMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
150-1000 uM [U-99% 15N] ARC92VBD, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM ARC92VBD, 100% D2O100% D2O
3200-1000 uM [U-99% 13C; U-99% 15N] ARC92VBD, 95% H2O/5% D2O95% H2O/5% D2O
4700 uM [U-100% 13C; U-100% 15N; U-80% 2H] ARC92VBD, 95% H2O/5% D2O95% H2O/5% D2O
5700 uM [ILV-100% 13C1H; U-100% 15N; U-100% 2H] ARC92VBD, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMARC92VBD-1[U-99% 15N]50-10001
1.0 mMARC92VBD-22
uMARC92VBD-3[U-99% 13C; U-99% 15N]200-10003
700 uMARC92VBD-4[U-100% 13C; U-100% 15N; U-80% 2H]4
700 uMARC92VBD-5[ILV-100% 13C1H; U-100% 15N; U-100% 2H]5
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA6001
Varian InovaVarianINOVA5002
Bruker AvanceBrukerAVANCE9003
Bruker AvanceBrukerAVANCE7504

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1 / Details: CYANA calculation, CNS in water box
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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