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BMRB: 16209

2KGG

Solution Structure of JARID1A C-terminal PHD finger

Authors

Song, J., Wang, Z., Patel, D.J.

Assembly

JARID1A PHD finger 3

Entity

1. JARID1A PHD finger 3 (polymer, Thiol state: free and other bound), 52 monomers, 5798.455 Da Detail

SVCAAQNCQR PCKDKVDWVQ CDGGCDEWFH QVCVGVSPEM AENEDYICIN CA

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

5929.273 Da

Max. entity weight

5798.455 Da

Entity Connection

na 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS3:SG	2:ZN1:ZN
2	na	sing	1:CYS8:SG	2:ZN1:ZN
3	na	sing	1:HIS30:NE2	2:ZN1:ZN
4	na	sing	1:CYS33:SG	2:ZN1:ZN
5	na	sing	1:CYS21:SG	2:ZN1:ZN
6	na	sing	1:CYS25:SG	2:ZN1:ZN
7	na	sing	1:CYS48:SG	2:ZN1:ZN
8	na	sing	1:CYS51:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.1 %, Completeness: 92.9 %, Completeness (bb): 95.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.9 % (525 of 565)	91.8 % (268 of 292)	93.5 % (200 of 214)	96.6 % (57 of 59)
Backbone	95.1 % (293 of 308)	96.2 % (101 of 105)	94.1 % (144 of 153)	96.0 % (48 of 50)
Sidechain	91.5 % (280 of 306)	89.3 % (167 of 187)	94.5 % (104 of 110)	100.0 % (9 of 9)
Aromatic	80.4 % (37 of 46)	82.6 % (19 of 23)	76.2 % (16 of 21)	100.0 % (2 of 2)
Methyl	100.0 % (40 of 40)	100.0 % (20 of 20)	100.0 % (20 of 20)

1. JARID1A PHD finger 3

SVCAAQNCQR PCKDKVDWVQ CDGGCDEWFH QVCVGVSPEM AENEDYICIN CA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2-0.5 mM
2	sodium phosphate	natural abundance	20 mM
3	ZnCl2	natural abundance	1 mM
4	DTT	natural abundance	5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 10 mM MOPS, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O, 200 mM NaCl, 12 mg/ml of bacteriophage Pf1

#	Name	Isotope labeling	Concentration
7	JARID1A PHD finger 3	[U-100% 15N]	0.2-0.5 mM
8	MOPS	natural abundance	10 mM
9	ZnCl2	natural abundance	1 mM
10	DTT	natural abundance	5 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %
13	NaCl	natural abundance	200 mM
14	bacteriophage Pf1	natural abundance	12 mg/mL

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.58 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.58 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.08 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KGG, Strand ID: A Detail

Release date

2009-05-28

Citation

Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger
Wang, G.G., Song, J., Wang, Z., Dormann, H.L., Casadio, F., Li, H., Luo, J., Patel, D.J., Allis, C.D.
Nature (2009), 459, 847-851, PubMed 19430464 , DOI 10.1038/nature08036 , Abstract

Related entities 1. JARID1A PHD finger 3, : 1 : 3 : 3 : 134 entities Detail

Interaction partners 1. JARID1A PHD finger 3, : 14 interactors Detail

More details for 14 interactors identified by 7 citations

Experiments performed 10 experiments Detail

1 1H,15N-HSQC