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- PDB-8j9a: Solution structure of ABD3 (residues 453-561) of human MED15 isoform 2 -

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Basic information

Entry
Database: PDB / ID: 8j9a
TitleSolution structure of ABD3 (residues 453-561) of human MED15 isoform 2
ComponentsMediator of RNA polymerase II transcription subunit 15
KeywordsTRANSCRIPTION / Mediator of RNA polymerase II transcription subunit 15
Function / homology
Function and homology information


core mediator complex / Generic Transcription Pathway / RSV-host interactions / somatic stem cell population maintenance / 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 coregulator activity / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation ...core mediator complex / Generic Transcription Pathway / RSV-host interactions / somatic stem cell population maintenance / 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 coregulator activity / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / nucleoplasm / membrane / nucleus / cytoplasm
Similarity search - Function
Mediator of RNA polymerase II transcription subunit 15 / : / : / ARC105/Med15 mediator subunit N-terminal KIX domain / ARC105/Med15 mediator subunit central domain / ARC105/Med15 mediator subunit C-terminal domain / Coactivator CBP, KIX domain superfamily
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsZhang, H. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82172299 China
CitationJournal: To Be Published
Title: Solution structure of ABD3 (residues 453-561) of human MED15 isoform 2
Authors: Zhang, H. / Li, Y.
History
DepositionMay 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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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 15


Theoretical massNumber of molelcules
Total (without water)13,4061
Polymers13,4061
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mediator of RNA polymerase II transcription subunit 15 / Activator-recruited cofactor 105 kDa component / ARC105 / CTG repeat protein 7a / Mediator complex ...Activator-recruited cofactor 105 kDa component / ARC105 / CTG repeat protein 7a / Mediator complex subunit 15 / Positive cofactor 2 glutamine/Q-rich-associated protein / PC2 glutamine/Q-rich-associated protein / TPA-inducible gene 1 protein / TIG-1 / Trinucleotide repeat-containing gene 7 protein


Mass: 13405.515 Da / Num. of mol.: 1 / Fragment: activator-binding domain 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED15, ARC105, CTG7A, PCQAP, TIG1, TNRC7 / Plasmid: pET-30a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RN5

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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
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D CBCA(CO)NH
151isotropic13D CBCANH
161isotropic13D HNCA
171isotropic13D HN(CO)CA
181isotropic13D HNCO
191isotropic13D HN(CA)CO
1101isotropic13D HBHA(CO)NH
1111isotropic13D C(CO)NH
1121isotropic13D H(CCO)NH
1131isotropic13D 1H-15N NOESY
1141isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] MED15_ABD3, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 6 % v/v D2O, 94% H2O/6% D2O
Label: 15N/13C_sample / Solvent system: 94% H2O/6% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMED15_ABD3[U-99% 13C; U-99% 15N]1
20 mMHEPESnatural abundance1
200 mMsodium chloridenatural abundance1
1 mMTCEPnatural abundance1
6 % v/vD2Onatural abundance1
Sample conditionsIonic strength: 200 mM / Label: condition_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
ARIA2alphaWolfgang Rieping, Michael Habeck, Benjamin Bardiaux, Aymeric Bernard, Therese E. Malliavin, Michael Nilgesstructure calculation
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA2alphaWolfgang Rieping, Michael Habeck, Benjamin Bardiaux, Aymeric Bernard, Therese E. Malliavin, Michael Nilgesrefinement
Refinement
MethodSoftware ordinal
simulated annealing2
torsion angle dynamics6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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