BMRB Entry 15001

Name: Structures and chemical shift assignments for the ADD domain of the ATRX protein
Published: 2007-06-18

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PDB ID: 2ld1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15001
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Structures and chemical shift assignments for the ADD domain of the ATRX protein PubMed: 17609377

Deposition date: 2006-09-13 Original release date: 2007-06-18

Authors: Yang, Ji-Chun; Neuhaus, David

Citation: Argentaro, Anthony; Yang, Ji-Chun; Chapman, Lynda; Kowalczyk, Monika; Gibbons, Richard; Higgs, Douglas; Neuhaus, David; Rhodes, Daniela. "Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX" Proc. Natl. Acad. Sci. U. S. A. 104, 11939-11944 (2007).

Assembly members:
ADD_domain_156-296, polymer, 142 residues, Formula weight is not available
ZN, non-polymer, 65.409 Da.

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

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
ADD_domain_156-296: GAMADKRGDGLHGIVSCTAC GQQVNHFQKDSIYRHPSLQV LICKNCFKYYMSDDISRDSD GMDEQCRWCAEGGNLICCDF CHNAFCKKCILRNLGRKELS TIMDENNQWYCYICHPEPLL DLVTACNSVFENLEQLLQQN KK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	399
15N chemical shifts	139
1H chemical shifts	852

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	protein chain	1
2	zinc 1	2
3	zinc 2	2
4	zinc 3	2

Entities:

Entity 1, protein chain 142 residues - Formula weight is not available

1

GLY

ALA

MET

ALA

ASP

LYS

ARG

GLY

ASP

GLY

2

LEU

HIS

GLY

ILE

VAL

SER

CYS

THR

ALA

CYS

3

GLY

GLN

VAL

ASN

HIS

PHE

GLN

LYS

ASP

4

SER

ILE

TYR

ARG

HIS

PRO

SER

LEU

GLN

VAL

5

LEU

ILE

CYS

LYS

ASN

CYS

PHE

LYS

TYR

6

MET

SER

ASP

ILE

SER

ARG

ASP

SER

ASP

7

GLY

MET

ASP

GLU

GLN

CYS

ARG

TRP

CYS

ALA

8

GLU

GLY

ASN

LEU

ILE

CYS

ASP

PHE

9

CYS

HIS

ASN

ALA

PHE

CYS

LYS

CYS

ILE

10

LEU

ARG

ASN

LEU

GLY

ARG

LYS

GLU

LEU

SER

11

THR

ILE

MET

ASP

GLU

ASN

GLN

TRP

TYR

12

CYS

TYR

ILE

CYS

HIS

PRO

GLU

PRO

LEU

13

ASP

LEU

VAL

THR

ALA

CYS

ASN

SER

VAL

PHE

14

GLU

ASN

LEU

GLU

GLN

LEU

GLN

ASN

15

LYS

Entity 2, zinc 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: ADD domain 156-296, [U-15N], 0.6 – 0.8 mM; TRIS, none, 20 mM; DTT, none, 1 mM; zinc chloride, none, 100 uM; sodium chloride, none, 0.5 M

sample_2: ADD domain 156-296, [U-13C; U-15N], 0.3 – 0.4 mM; TRIS, none, 20 mM; DTT, none, 1 mM; zinc chloride, none, 100 uM; sodium chloride, none, 0.5 M

sample_conditions_1: ionic strength: 0.5 M; pH: 6.7; pressure: 1 atm; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
HNHAHB	sample_2	isotropic	sample_conditions_1
HN(CO)HAHB	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1

Software:

xwinnmr v3.5, Bruker Biospin - collection, processing

SPARKY, T Goddard - data analysis, peak picking

X-PLOR v3.8, AT Brunger - refinement, structure solution

NMR spectrometers:

Bruker Avance 800 MHz
Bruker DRX 500 MHz

BMRB	17569
PDB	2JM1 2LBM 2LD1
DBJ	BAC28096 BAC40142 BAC81110 BAC81111 BAC81112
EMBL	CAB90351 CAI40710 CAI42674 CAI42675 CAI43115
GB	AAB40698 AAB40699 AAB40700 AAB49969 AAB49970
REF	NP_000480 NP_001009018 NP_033556 NP_612114 XP_001099671
SP	P46100 Q61687 Q7YQM3 Q7YQM4
TPG	DAA12976 DAA12977

Biological Magnetic Resonance Data Bank