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- PDB-2lri: NMR structure of the second PHD finger of AIRE (AIRE-PHD2) -

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Basic information

Entry
Database: PDB / ID: 2lri
TitleNMR structure of the second PHD finger of AIRE (AIRE-PHD2)
ComponentsAutoimmune regulator
KeywordsTRANSCRIPTION / Zn binding protein domain / APECED
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 1
AuthorsGaetani, M. / Chignola, F. / Mollica, L. / Quilici, G. / Mannella, V. / Spiliotopoulos, D. / Musco, G.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: AIRE-PHD fingers are structural hubs to maintain the integrity of chromatin-associated interactome.
Authors: Gaetani, M. / Matafora, V. / Saare, M. / Spiliotopoulos, D. / Mollica, L. / Quilici, G. / Chignola, F. / Mannella, V. / Zucchelli, C. / Peterson, P. / Bachi, A. / Musco, G.
History
DepositionApr 3, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / 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_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Autoimmune regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9423
Polymers6,8111
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)50 / 50structures 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: 6810.685 Da / Num. of mol.: 1 / Fragment: PHD-type 2 Zinc finger residues 423-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIRE, APECED / Production host: Escherichia coli (E. coli) / 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
1132D 1H-15N HSQC
1212D 1H-13C HSQC
1342D 1H-1H TOCSY
1452D 1H-1H TOCSY
1542D 1H-1H NOESY
1652D 1H-1H NOESY
1713D CBCA(CO)NH
1813D C(CO)NH
1913D HNCO
11013D HNCA
11113D H(CCO)NH
11223D (H)CCH-TOCSY
11333D HNHA
11433D 1H-15N NOESY
11523D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-0.8 mM [U-100% 13C; U-100% 15N] AIRE-PHD2, 50 uM ZINC ION, 5 mM DTT, 50 mM sodium phosphate, 0.15 M sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.4-0.8 mM [U-100% 13C; U-100% 15N] AIRE-PHD2, 5 mM DTT, 50 uM ZINC ION, 50 mM sodium phosphate, 0.15 M sodium chloride, 0.02 % sodium azide, 100% D2O100% D2O
30.4-0.8 mM [U-100% 15N] AIRE-PHD2, 5 mM DTT, 50 uM ZINC ION, 50 mM sodium phosphate, 0.15 M sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
40.4-0.8 mM AIRE-PHD2, 5 mM DTT, 50 uM ZINC ION, 50 mM sodium phosphate, 0.15 M sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
50.4-0.8 mM AIRE-PHD2, 5 mM DTT, 50 uM ZINC ION, 50 mM sodium phosphate, 0.15 M sodium chloride, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMAIRE-PHD2-1[U-100% 13C; U-100% 15N]0.4-0.81
50 uMZINC ION-21
5 mMDTT-31
50 mMsodium phosphate-41
0.15 Msodium chloride-51
0.02 %sodium azide-61
mMAIRE-PHD2-7[U-100% 13C; U-100% 15N]0.4-0.82
5 mMDTT-82
50 uMZINC ION-92
50 mMsodium phosphate-102
0.15 Msodium chloride-112
0.02 %sodium azide-122
mMAIRE-PHD2-13[U-100% 15N]0.4-0.83
5 mMDTT-143
50 uMZINC ION-153
50 mMsodium phosphate-163
0.15 Msodium chloride-173
0.02 %sodium azide-183
mMAIRE-PHD2-190.4-0.84
5 mMDTT-204
50 uMZINC ION-214
50 mMsodium phosphate-224
0.15 Msodium chloride-234
0.02 %sodium azide-244
mMAIRE-PHD2-250.4-0.85
5 mMDTT-265
50 uMZINC ION-275
50 mMsodium phosphate-285
0.15 Msodium chloride-295
0.02 %sodium azide-305
Sample conditionsIonic strength: 0.15 / pH: 6.5 / 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
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
CCPNMR2.1CCPNchemical shift assignment
ARIA2.3Linge, 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: 50 / Conformers submitted total number: 50

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