BMRB Entry 16209

Name: Solution Structure of JARID1A C-terminal PHD finger
Published: 2009-05-29

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PDB ID: 2kgg
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/BMR16209
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of JARID1A C-terminal PHD finger

Deposition date:

2009-03-11

Original release date:

2009-05-29

Authors:

Song, Jikui; Wang, Zhanxin; Patel, Dinshaw

Citation:

Citation: Wang, Gang; Song, Jikui; Wang, Zhanxin; Dormann, Holger; Casadio, Fabio; Li, Haitao; Luo, Jun-Li; Patel, Dinshaw; Allis, C.. "Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger" Nature 459, 847-851 (2009).
PubMed: 19430464

Assembly members:

Assembly members:
JARID1A_PHD_finger_3, polymer, 52 residues, 5802.505 Da.
ZN, 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: pRSFDuet-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
JARID1A_PHD_finger_3: SVCAAQNCQRPCKDKVDWVQ CDGGCDEWFHQVCVGVSPEM AENEDYICINCA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	199
15N chemical shifts	57
1H chemical shifts	309

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	JARID1A PHD finger 3	1
2	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, JARID1A PHD finger 3 52 residues - 5802.505 Da.

1

SER

VAL

CYS

ALA

GLN

ASN

CYS

GLN

ARG

2

PRO

CYS

LYS

ASP

LYS

VAL

ASP

TRP

VAL

GLN

3

CYS

ASP

GLY

CYS

ASP

GLU

TRP

PHE

HIS

4

GLN

VAL

CYS

VAL

GLY

VAL

SER

PRO

GLU

MET

5

ALA

GLU

ASN

GLU

ASP

TYR

ILE

CYS

ILE

ASN

6

CYS

ALA

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: JARID1A PHD finger 3, [U-100% 13C; U-100% 15N], 0.2-0.5 mM; sodium phosphate 20 mM; ZnCl2 1 mM; DTT 5 mM; H2O 90%; D2O 10%

sample_2: JARID1A PHD finger 3, [U-100% 15N], 0.2-0.5 mM; MOPS 10 mM; ZnCl2 1 mM; DTT 5 mM; H2O 90%; D2O 10%; NaCl 200 mM; bacteriophage Pf1 12 mg/ml

sample_conditions_1: ionic strength: 20 mM; pH: 7.0; pressure: 1 atm; temperature: 293.2 K

sample_conditions_2: ionic strength: 200 mM; pH: 7.0; pressure: 1 atm; temperature: 298.2 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H,15N-HSQC	sample_1	isotropic	sample_conditions_1
1H,13C-HSQC	sample_1	isotropic	sample_conditions_1
HNCACB	sample_1	isotropic	sample_conditions_1
HBHACONH	sample_1	isotropic	sample_conditions_1
CBCACONH	sample_1	isotropic	sample_conditions_1
2D 1H, 1H-NOESY	sample_1	isotropic	sample_conditions_1
HCCHTOCSY	sample_1	isotropic	sample_conditions_1
15N-EDITED 1H,1H-NOESY	sample_1	isotropic	sample_conditions_1
13C-EDITED 1H,1H-NOESY	sample_1	isotropic	sample_conditions_1
15N IPAP HSQC	sample_2	isotropic	sample_conditions_2

Software:

CNS, Brunger A. T. et.al. - refinement

NMR spectrometers:

Bruker DMX 800 MHz

BMRB	16210
PDB	2KGG 2KGI 3GL6
DBJ	BAE06081 BAG10524
GB	ACH71258 ELK02599 ELK24529 ELV13200 EOB07246
REF	NP_001036068 NP_001264106 XP_001373115 XP_001914992 XP_002712829
SP	P29375
AlphaFold	P29375