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- PDB-8y4l: The ACID domain of aMED25 -

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Basic information

Entry
Database: PDB / ID: 8y4l
TitleThe ACID domain of aMED25
ComponentsMediator of RNA polymerase II transcription subunit 25
KeywordsTRANSCRIPTION / Activator-interacting domain / transcription activation / plant protein
Function / homology
Function and homology information


trichome papilla formation / trichome branching / positive regulation of defense response / response to red light / positive regulation of flower development / regulation of flower development / red, far-red light phototransduction / jasmonic acid mediated signaling pathway / response to far red light / flower development ...trichome papilla formation / trichome branching / positive regulation of defense response / response to red light / positive regulation of flower development / regulation of flower development / red, far-red light phototransduction / jasmonic acid mediated signaling pathway / response to far red light / flower development / mediator complex / defense response to fungus / transcription coactivator activity / positive regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
Mediator of RNA polymerase II transcription subunit 25, von Willebrand factor type A domain / Mediator complex subunit 25 von Willebrand factor type A
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 25
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / na
AuthorsXiong, Y. / Zhu, J. / Yang, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21991082 China
National Natural Science Foundation of China (NSFC)21921004 China
Chinese Academy of SciencesXDB0540203 China
CitationJournal: To Be Published
Title: The ACID domain of aMED25
Authors: Xiong, Y. / Zhu, J. / Yang, Y.
History
DepositionJan 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: 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 25


Theoretical massNumber of molelcules
Total (without water)14,5221
Polymers14,5221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mediator of RNA polymerase II transcription subunit 25 / AtMED25 / Phytochrome and flowering time 1 protein / Phytochrome and flowering time regulatory protein 1


Mass: 14521.814 Da / Num. of mol.: 1 / Fragment: ACID domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MED25, MED25_1, PFT1, At1g25540, F2J7.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7XYY2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aromatic
131isotropic12D 1H-13C HSQC aliphatic
141isotropic13D HNCO
151isotropic13D HN(CA)CO
191isotropic13D HNCA
181isotropic13D HN(CO)CA
171isotropic13D HN(CA)CB
161isotropic13D CBCA(CO)NH
1131isotropic13D HBHA(CO)NH
1121isotropic1CC(CO)NH
1111isotropic33D 1H-15N NOESY
1141isotropic23D 1H-13C NOESY aliphatic
1101isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 500 mM NA- sodium chloride, 50 mM NA- NaH2PO4, 2 % NA- sodium azide, 5 uM NA- DTT, 4.0 mg/mL [U-100% 13C; U-100% 15N] Protein, 90% H2O/10% D2O
Label: 13C,15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 mMsodium chlorideNA-1
50 mMNaH2PO4NA-1
2 %sodium azideNA-1
5 uMDTTNA-1
4.0 mg/mLProtein[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 1 M / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE IIIBrukerAVANCE III8503

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
FMCGUIBrungerrefinement
SparkyGoddardpeak picking
RefinementMethod: na / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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