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- PDB-2l23: NMR structure of the ACID (ACtivator Interacting Domain) of the h... -

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Basic information

Entry
Database: PDB / ID: 2l23
TitleNMR structure of the ACID (ACtivator Interacting Domain) of the human mediator Med25 protein
ComponentsMediator of RNA polymerase II transcription subunit 25
KeywordsTRANSCRIPTION / human mediator complex / Pancreatic tumor overexpressed domain
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 / 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 / mediator complex / nuclear retinoic acid receptor binding / 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 / torsion angle dynamics
AuthorsBontems, F. / Monte, D. / Dewitte, F. / Villeret, V.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: NMR structure of the human Mediator MED25 ACID domain.
Authors: Bontems, F. / Verger, A. / Dewitte, F. / Lens, Z. / Baert, J.L. / Ferreira, E. / Launoit, Y. / Sizun, C. / Guittet, E. / Villeret, V. / Monte, D.
History
DepositionAug 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: database_2 / pdbx_nmr_exptl ...database_2 / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct / 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_exptl.conditions_id / _pdbx_nmr_exptl.solution_id / _pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_software.version / _struct.pdbx_model_details / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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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)19,2201
Polymers19,2201
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)20 / 20all calculated structures submitted
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: 19220.330 Da / Num. of mol.: 1 / Fragment: ACID domain, UNP residues 391-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACID1, ARC92, MED25, PTOV2, TCBAP0758 / Plasmid: pET / 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
1142D 1H-15N HSQC
1232D 1H-13C HSQC
1313D HNCA
1413D HN(CA)CB
1513D HNCO
1613D CBCA(CO)NH
1713D HNHA
1833D (H)CCH-TOCSY
1923D 1H-15N NOESY
11033D 1H- 13CALI NOESY
11133D 1H-13CARO NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.3-0.5 MM [U-98% 13C U-98% 15N] MED25, 10 MM SODIUM PHOSPHATE, 100 MM SODIUM CHLORIDE, 5 MM DTT, 90% H2O/ 10% D2Osample_190% H2O/10% D2O
solution20.3-0.5 MM [U-100% 15N] MED25, 10 MM SODIUM PHOSPHATE, 100 MM SODIUM CHLORIDE, 5 MM DTT, 90% H2O/10% D2Osample_290% H2O/10% D2O
solution30.3-0.5 MM [U-95% 13C] MED25, 10 MM SODIUM PHOSPHATE, 100 MM SODIUM CHLORIDE, 5 MM DTT, 100% D2Osample_3100% D2O
solution40.2 MM [U-100% 15N] MED25, 10 MM SODIUM PHOSPHATE, 100 MM SODIUM CHLORIDE, 5 MM DTT, 100% D2Osample_4100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMMed25[U-98% 13C; U-98% 15N]0.3-0.51
10 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
5 mMDTTnatural abundance1
mMMed25[U-100% 15N]0.3-0.52
10 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
5 mMDTTnatural abundance2
mMMed25[U-95% 13C]0.3-0.53
10 mMsodium phosphatenatural abundance3
100 mMsodium chloridenatural abundance3
5 mMDTTnatural abundance3
0.2 mMMed25[U-100% 15N]4
10 mMsodium phosphatenatural abundance4
100 mMsodium chloridenatural abundance4
5 mMDTTnatural abundance4
Sample conditionsIonic strength: 120 / pH: 6.75 / Pressure: AMBIENT / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE IIBrukerAVANCE II6002
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CcpNmr AnalysisCCPN Projectchemical shift assignment
CcpNmr AnalysisCCPN Projectpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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