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- PDB-1xwh: NMR structure of the first phd finger of autoimmune regulator pro... -

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Basic information

Entry
Database: PDB / ID: 1xwh
TitleNMR structure of the first phd finger of autoimmune regulator protein (AIRE1): insights into apeced
ComponentsAutoimmune regulator
KeywordsTRANSCRIPTION / PHD domain / Zn binding domain / APECED / nucleosome / E3 ligase
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 / Structures were calculated using ARIA (1.2) in combination with CNS
AuthorsBottomley, M.J. / Stier, G. / Krasotkina, J. / Legube, G. / Simon, B. / Akhtar, A. / Sattler, M. / Musco, G.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: NMR structure of the first PHD finger of autoimmune regulator protein (AIRE1). Insights into autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) disease
Authors: Bottomley, M.J. / Stier, G. / Pennacchini, D. / Legube, G. / Simon, B. / Akhtar, A. / Sattler, M. / Musco, G.
History
DepositionNov 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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_software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2763
Polymers7,1451
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 / 100structures 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 PHDdomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: aire1 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43918
#2: 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 15N-separated NOESY
2223D 13C-separated NOESY
131HNHA
NMR detailsText: The first 4 amino acids (GAMA) do not belong to AIRE1 sequence.

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Sample preparation

DetailsContents: 1mM AIRE1-PHD1, U-15N,13C; 20mM phosphate buffer, pH 6.3, 150mM NaCl, 5mM DTT
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 150mM Nacl, 20mM phosphate buffer / pH: 6.3 / Pressure: ambient / Temperature: 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3Delaglio et al.processing
CNS1refinement
ARIAaria1.2Nilges et al.structure solution
XEASY1.2Bartels et al.data analysis
RefinementMethod: Structures were calculated using ARIA (1.2) in combination with CNS
Software ordinal: 1
Details: The AIRE1-PHD1 solution structure was determined from a total of 970 NMR-derived distance and 66 dihedral angle restraints, 44 residual dipolar
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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