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- PDB-6zv3: TFIIS N-terminal domain (TND) from human MED26 -

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Basic information

Entry
Database: PDB / ID: 6zv3
TitleTFIIS N-terminal domain (TND) from human MED26
ComponentsMediator of RNA polymerase II transcription subunit 26
KeywordsTRANSCRIPTION / transcription elongation
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 / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / 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 / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / 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 N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / 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 / torsion angle dynamics / molecular dynamics
AuthorsVeverka, V.
CitationJournal: Science / Year: 2021
Title: A ubiquitous disordered protein interaction module orchestrates transcription elongation.
Authors: Cermakova, K. / Demeulemeester, J. / Lux, V. / Nedomova, M. / Goldman, S.R. / Smith, E.A. / Srb, P. / Hexnerova, R. / Fabry, M. / Madlikova, M. / Horejsi, M. / De Rijck, J. / Debyser, Z. / ...Authors: Cermakova, K. / Demeulemeester, J. / Lux, V. / Nedomova, M. / Goldman, S.R. / Smith, E.A. / Srb, P. / Hexnerova, R. / Fabry, M. / Madlikova, M. / Horejsi, M. / De Rijck, J. / Debyser, Z. / Adelman, K. / Hodges, H.C. / Veverka, V.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Mediator of RNA polymerase II transcription subunit 26


Theoretical massNumber of molelcules
Total (without water)10,1841
Polymers10,1841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6440 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 100structures with the least restraint violations
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: 10183.872 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 (E. coli) / 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
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
171isotropic13D HBHA(CO)NH
161isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] MED26, 25 mM [U-2H] TRIS, 200 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O
Label: s1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMED26[U-13C; U-15N]1
25 mMTRIS[U-2H]1
200 mMsodium chloridenatural abundance1
1 mMTCEPnatural abundance1
Sample conditionsIonic strength: 225 mM / Label: c1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARAYASARArefinement
Refinement
MethodSoftware ordinal
torsion angle dynamics2
molecular dynamics3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 50

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