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- PDB-2ke1: Molecular Basis of non-modified histone H3 tail Recognition by th... -

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Basic information

Entry
Database: PDB / ID: 2ke1
TitleMolecular Basis of non-modified histone H3 tail Recognition by the First PHD Finger of Autoimmune Regulator
Components
  • Autoimmune regulator
  • H3K4me0
KeywordsGENE REGULATION / AIRE / PHD finger / Histone H3 / Disease mutation / Metal-binding / Nucleus / Transcription / Transcription regulation / Zinc / Zinc-finger
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 / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 1
AuthorsChignola, F. / Gaetani, M. / Rebane, A. / Org, T. / Mollica, L. / Zucchelli, C. / Spitaleri, A. / Mannella, V. / Peterson, P. / Musco, G.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation
Authors: Chignola, F. / Gaetani, M. / Rebane, A. / Org, T. / Mollica, L. / Zucchelli, C. / Spitaleri, A. / Mannella, V. / Peterson, P. / Musco, G.
History
DepositionJan 22, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autoimmune regulator
B: H3K4me0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4264
Polymers8,2952
Non-polymers1312
Water00
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: 7145.102 Da / Num. of mol.: 1 / Fragment: First PHD domain, UNP residues 293-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O43918
#2: Protein/peptide H3K4me0


Mass: 1150.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized peptide
#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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D HNCA
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D HNHA
1713D H(CCO)NH
1812D 1H-1H NOESY
1923D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1-0.5 mM [U-99% 13C; U-99% 15N] AIRE-PHD1-1, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-99% 13C; U-99% 15N] AIRE-PHD1+H3K4me0-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMAIRE-PHD1-1[U-99% 13C; U-99% 15N]0.1-0.51
0.5 mMAIRE-PHD1+H3K4me0-2[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 0.15 / pH: 6.3 / Pressure: ambient / Temperature: 295 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
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 / Representative conformer: 1

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