BMRB Entry 18374

Name: NMR structure of the second PHD finger of AIRE (AIRE-PHD2)
Published: 2012-10-12

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PDB ID: 2lri
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18374
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of the second PHD finger of AIRE (AIRE-PHD2)

Deposition date:

2012-04-03

Original release date:

2012-10-12

Authors:

Gaetani, Massimiliano; Chignola, Francesca; Mollica, Luca; Quilici, Giacomo; Mannella, Valeria; Spiliotopoulos, Dimitrios; Musco, Giovanna

Citation:

Citation: Gaetani, Massimiliano; Matafora, Vittoria; Saare, Mario; Spiliotopoulos, Dimitrios; Mollica, Luca; Quilici, Giacomo; Chignola, Francesca; Mannella, Valeria; Zucchelli, Chiara; Peterson, Part; Bachi, Angela; Musco, Giovanna. "AIRE-PHD fingers are structural hubs to maintain the integrity of chromatin-associated interactome." Nucleic Acids Res. 40, 11756-11768 (2012).
PubMed: 23074189

Assembly members:

Assembly members:
AIRE-PHD2, polymer, 66 residues, 6810.711 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-24d

Entity Sequences (FASTA):

Entity Sequences (FASTA):
AIRE-PHD2: GAMEGQQNLAPGARCGVCGD GTDVLRCTHCAAAFHWRCHF PAGTSRPGTGLRCRSCSGDV TPAPVE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	192
15N chemical shifts	62
1H chemical shifts	381

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	AIRE-PHD2	1
2	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, AIRE-PHD2 66 residues - 6810.711 Da.

1

GLY

ALA

MET

GLU

GLY

GLN

ASN

LEU

ALA

2

PRO

GLY

ALA

ARG

CYS

GLY

VAL

CYS

GLY

ASP

3

GLY

THR

ASP

VAL

LEU

ARG

CYS

THR

HIS

CYS

4

ALA

PHE

HIS

TRP

ARG

CYS

HIS

PHE

5

PRO

ALA

GLY

THR

SER

ARG

PRO

GLY

THR

GLY

6

LEU

ARG

CYS

ARG

SER

CYS

SER

GLY

ASP

VAL

7

THR

PRO

ALA

PRO

VAL

GLU

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

AIRE-PHD2-H2O: AIRE-PHD2, [U-100% 13C; U-100% 15N], 0.4 – 0.8 mM; ZINC ION 50 uM; DTT 5 mM; sodium phosphate 50 mM; sodium chloride 0.15 M; sodium azide 0.02%; D2O 10%; H2O 90%

AIRE-PHD2-D2O: AIRE-PHD2, [U-100% 13C; U-100% 15N], 0.4 – 0.8 mM; DTT 5 mM; ZINC ION 50 uM; sodium phosphate 50 mM; sodium chloride 0.15 M; sodium azide 0.02%; D2O 100%

15N-PHD2_H2O: AIRE-PHD2, [U-100% 15N], 0.4 – 0.8 mM; DTT 5 mM; ZINC ION 50 uM; sodium phosphate 50 mM; sodium chloride 0.15 M; sodium azide 0.02%; D2O 10%; H2O 90%

Unlabel_PHD2_H2O: AIRE-PHD20.4 – 0.8 mM; DTT 5 mM; ZINC ION 50 uM; sodium phosphate 50 mM; sodium chloride 0.15 M; sodium azide 0.02%; D2O 10%; H2O 90%

Unlabel_PHD2_D2O: AIRE-PHD20.4 – 0.8 mM; DTT 5 mM; ZINC ION 50 uM; sodium phosphate 50 mM; sodium chloride 0.15 M; sodium azide 0.02%; D2O 100%

AIRE-PHD2_condition: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 295 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	15N-PHD2_H2O	isotropic	AIRE-PHD2_condition
2D 1H-13C HSQC	AIRE-PHD2-H2O	isotropic	AIRE-PHD2_condition
2D 1H-1H TOCSY	Unlabel_PHD2_H2O	isotropic	AIRE-PHD2_condition
2D 1H-1H TOCSY	Unlabel_PHD2_D2O	isotropic	AIRE-PHD2_condition
2D 1H-1H NOESY	Unlabel_PHD2_H2O	isotropic	AIRE-PHD2_condition
2D 1H-1H NOESY	Unlabel_PHD2_D2O	isotropic	AIRE-PHD2_condition
3D CBCA(CO)NH	AIRE-PHD2-H2O	isotropic	AIRE-PHD2_condition
3D C(CO)NH	AIRE-PHD2-H2O	isotropic	AIRE-PHD2_condition
3D HNCO	AIRE-PHD2-H2O	isotropic	AIRE-PHD2_condition
3D HNCA	AIRE-PHD2-H2O	isotropic	AIRE-PHD2_condition
3D H(CCO)NH	AIRE-PHD2-H2O	isotropic	AIRE-PHD2_condition
3D HCCH-TOCSY	AIRE-PHD2-D2O	isotropic	AIRE-PHD2_condition
3D HNHA	15N-PHD2_H2O	isotropic	AIRE-PHD2_condition
3D 1H-15N NOESY	15N-PHD2_H2O	isotropic	AIRE-PHD2_condition
3D 1H-13C NOESY	AIRE-PHD2-D2O	isotropic	AIRE-PHD2_condition

Software:

ARIA2.3, Linge, O'Donoghue and Nilges - structure solution

ANALYSIS, CCPN - chemical shift assignment

NMR spectrometers:

Bruker Avance 600 MHz

PDB	2LRI
DBJ	BAA23988 BAA23989 BAA23990 BAA23991 BAA95560
EMBL	CAB10790
GB	AAI37269 AAI37271 AIC54015 EAX09441 EAX09443
REF	NP_000374 XP_004062941 XP_008975805 XP_009439558 XP_011527853
SP	O43918
AlphaFold	O43918