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- PDB-2l6u: Solution NMR Structure of Med25(391-543) Comprising the Activator... -

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Basic information

Entry
Database: PDB / ID: 2l6u
TitleSolution NMR Structure of Med25(391-543) Comprising the Activator-Interacting Domain (ACID) of Human Mediator Subuniti 25. Northeast Structural Genomics Consortium Target HR6188A
ComponentsMediator complex subunit MED25Mediator (coactivator)
KeywordsTRANSCRIPTION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative / ARC92 / ACID / PTOV
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 / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Ryuechan, W.T. / Sukumaran, D.K. / Shastry, R. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Eletsky, A. / Ryuechan, W.T. / Sukumaran, D.K. / Shastry, R. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Struct.Funct.Genom. / Year: 2011
Title: Solution NMR structure of MED25(391-543) comprising the activator-interacting domain (ACID) of human mediator subunit 25.
Authors: Eletsky, A. / Ruyechan, W.T. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Szyperski, T.
History
DepositionNov 24, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 28, 2011Group: Database references
Revision 1.3Feb 22, 2012Group: Structure summary
Revision 1.4Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_representative / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_representative.selection_criteria ..._pdbx_database_status.status_code_cs / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5Aug 18, 2021Group: Database references / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling
Revision 1.6Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Mediator complex subunit MED25


Theoretical massNumber of molelcules
Total (without water)18,6381
Polymers18,6381
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Mediator complex subunit MED25 / Mediator (coactivator)


Mass: 18637.617 Da / Num. of mol.: 1 / Fragment: ACID domain residues 391-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED25 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q71SY5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HN(CA)CO
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HBHA(CO)NH
1913D HNCA
11012D 1H-13C CT-HSQC aliphatic
11112D 1H-13C CT-HSQC aromatic
11211D 15N T1
11311D 15N T2
11413D (H)CCH-TOCSY aliphatic
11513D (H)CCH-COSY aliphatic
11613D (H)CCH-COSY aromatic
11712D 1H-15N LR-HSQC for histidines
11812D (HB)CB(CGCDCE)HDHE
11922D 1H-13C CT-HSQC methyl

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 MM [U-100% 13C U-100% 15N] HR6188A, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution20.4 MM [U-5% 13C U-100% 15N] HR6188A, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMHR6188A[U-100% 13C; U-100% 15N]1
20 mMMESnatural abundance1
100 mMsodium chloridenatural abundance1
5 mMcalcium chloridenatural abundance1
10 mMDTTnatural abundance1
0.02 %sodium azidenatural abundance1
0.4 mMHR6188A[U-5% 13C; U-100% 15N]2
20 mMMESnatural abundance2
100 mMsodium chloridenatural abundance2
5 mMcalcium chloridenatural abundance2
10 mMDTTnatural abundance2
0.02 %sodium azidenatural abundance2
Sample conditionspH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASY1.3.13Bartels et al.data analysis
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
VnmrJ2.2DVariancollection
PROSA6.4Guntertprocessing
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND AUTOSTRUCTURE IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ...Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND AUTOSTRUCTURE IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD.
NMR constraintsNOE constraints total: 2684 / NOE intraresidue total count: 614 / NOE long range total count: 984 / NOE medium range total count: 460 / NOE sequential total count: 626 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 60 / Protein psi angle constraints total count: 60
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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