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- PDB-5odd: HUMAN MED26 N-TERMINAL DOMAIN (1-92) -

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Basic information

Entry
Database: PDB / ID: 5odd
TitleHUMAN MED26 N-TERMINAL DOMAIN (1-92)
ComponentsMediator of RNA polymerase II transcription subunit 26
KeywordsTRANSCRIPTION / Mediator complex transcriptional regulation
Function / homology
Function and homology information


core mediator complex / mediator complex / Generic Transcription Pathway / RSV-host interactions / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / PPARA activates gene expression ...core mediator complex / mediator complex / Generic Transcription Pathway / RSV-host interactions / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / transcription coactivator activity / positive regulation of gene expression / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Mediator complex subunit 26, C-terminal domain / Mediator complex subunit 26, middle domain / Mediator of RNA polymerase II transcription subunit 26 / Mediator complex subunit 26 C-terminal / Mediator complex subunit 26 middle domain / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / TFIIS N-terminal domain profile. / TFIIS/LEDGF domain superfamily
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsLens, Z. / Cantrelle, F.-X. / Perruzini, R. / Dewitte, F. / Hanoulle, X. / Villeret, V. / Verger, A. / Landrieu, I.
Citation
Journal: Biomol.Nmr Assign. / Year: 2016
Title: 1H, 15N and 13C assignments of the N-terminal domain of the Mediator complex subunit MED26.
Authors: Peruzzini, R. / Lens, Z. / Verger, A. / Dewitte, F. / Ferreira, E. / Baert, J.L. / Villeret, V. / Landrieu, I. / Cantrelle, F.X.
#1: Journal: Data in Brief / Year: 2017
Title: Nuclear magnetic resonance data on the interaction of MED26 N-terminal domain with peptide ligands from TAF7 and EAF1 proteins
Authors: Cantrelle, F.X. / Lens, Z. / Peruzzini, R. / Dewitte, F. / Ferreira, E. / Baert, J.L. / Monte, D. / Villeret, V. / Verger, A. / Landrieu, I.
History
DepositionJul 5, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionNov 29, 2017ID: 2MZO
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jan 29, 2020Group: Data collection / Database references / Category: citation / database_2 / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 26


Theoretical massNumber of molelcules
Total (without water)10,5571
Polymers10,5571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, 15N-Relaxation dynamics
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6470 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Mediator of RNA polymerase II transcription subunit 26 / Activator-recruited cofactor 70 kDa component / ARC70 / Cofactor required for Sp1 transcriptional ...Activator-recruited cofactor 70 kDa component / ARC70 / Cofactor required for Sp1 transcriptional activation subunit 7 / CRSP complex subunit 7 / Mediator complex subunit 26 / Transcriptional coactivator CRSP70


Mass: 10557.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED26, ARC70, CRSP7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O95402

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D HN(CA)CB
122isotropic13D HNCO
132isotropic13D HNCA
142isotropic23D 1H-13C NOESY aliphatic
152isotropic13D (H)CCH-TOCSY
162isotropic13D 1H-13C NOESY aromatic
183isotropic13D 1H-15N TOCSY
173isotropic12D 1H-15N HSQC
192isotropic12D 1H-13C HSQC aliphatic
1103isotropic13D 1H-15N NOESY
1113isotropic13D HNHA
1122isotropic13D HN(CO)CA
1133isotropic13D HBHA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution21.2 mM [U-13C; U-15N] MED26-NTD, 100% D2O20 mM Hepes, 100mM NaCl, 2.5 mM EDTA, 1 mM DTTU15N,13C-MED26100% D2O
solution31.2 mM [U-99% 15N] MED26-NTD, 95% H2O/5% D2O20 mM Hepes, 100mM NaCl, 2.5 mM EDTA, 1 mM DTTU15N-MED2695% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMMED26-NTD[U-13C; U-15N]2
1.2 mMMED26-NTD[U-99% 15N]3
Sample conditionsDetails: 20 mM Hepes, 100mM NaCl, 2.5 mM EDTA, 1 mM DTT / Ionic strength: 0.1 mM / Label: MED26 / pH: 6.8 / Pressure: AMBIENT Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCE IIIBrukerAVANCE III9002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger A. T. et.al.refinement
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
SPARTAShen and Baxchemical shift assignment
TopSpinBruker Biospinprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
CANDIDHerrmann, Guntert and Wuthrichchemical shift assignment
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: all restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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