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- PDB-2kft: NMR Solution structure of the first PHD finger domain of human Au... -

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Basic information

Entry
Database: PDB / ID: 2kft
TitleNMR Solution structure of the first PHD finger domain of human Autoimmune Regulator (AIRE) in complex with Histone H3(1-20Cys) Peptide
Components
  • Autoimmune regulator
  • Histone H3
KeywordsTRANSCRIPTION/PROTEIN BINDING / PHD Finger / Histone Code / AIRE / APECED / Transcription / Alternative splicing / Cytoplasm / Disease mutation / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Transcription regulation / Zinc / Zinc-finger / Chromosomal protein / Nucleosome core / TRANSCRIPTION-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


peripheral T cell tolerance induction / central tolerance induction to self antigen / regulation of thymocyte migration / thymus epithelium morphogenesis / negative thymic T cell selection / female germ cell nucleus / humoral immune response / translation regulator activity / positive regulation of chemokine production / male germ cell nucleus ...peripheral T cell tolerance induction / central tolerance induction to self antigen / regulation of thymocyte migration / thymus epithelium morphogenesis / negative thymic T cell selection / female germ cell nucleus / humoral immune response / translation regulator activity / positive regulation of chemokine production / male germ cell nucleus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / histone binding / transcription by RNA polymerase II / nuclear body / immune response / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Autoimmune regulator, AIRE / AIRE, PHD finger 2 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain ...Autoimmune regulator, AIRE / AIRE, PHD finger 2 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Autoimmune regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 20
AuthorsChakravarty, S. / Zeng, L. / Zhou, M.
CitationJournal: Structure / Year: 2009
Title: Structure and Site-Specific Recognition of Histone H3 by the PHD Finger of Human Autoimmune Regulator.
Authors: Chakravarty, S. / Zeng, L. / Zhou, M.M.
History
DepositionFeb 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autoimmune regulator
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4444
Polymers8,3142
Non-polymers1312
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Autoimmune regulator / / Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy protein / APECED protein


Mass: 6019.827 Da / Num. of mol.: 1 / Fragment: AIRE PHD-type 1 Zinc Finger
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIRE, APECED / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43918
#2: Protein/peptide Histone H3 /


Mass: 2293.715 Da / Num. of mol.: 1 / Fragment: Histone H3 1-20Cys N-terminal domain / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR Structure of AIRE PHD Finger in Complex with unmodified Histone H3 1-20 N-terminal tail
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY
1413D HN(COCA)CB
1513D HN(CO)CA
1612D DQF-COSY
1712D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 15N] AIRE PHD finger 1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: AIRE PHD finger 1 / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: 250 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesdata analysis
CNS1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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