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BMRB: 19913

2MNY

NMR Structure of KDM5B PHD1 finger

Authors

Zhang, Y., Yang, H.R., Guo, X., Rong, N.Y., Song, Y.J., Xu, Y.W., Lan, W.X., Xu, Y.H., Cao, C.Y.

Assembly

KDM5B PHD1 finger

Entity

1. PHD1 finger of KDM5B (polymer), 55 monomers, 6126.948 Da Detail

AVDLYVCLLC GSGNDEDRLL LCDGCDDSYH TFCLIPPLHD VPKGDWRCPK CLAQE

2. ZINC ION (non-polymer), 65.409 × 2 Da

Total weight

6257.766 Da

Max. entity weight

6126.948 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 83.1 %, Completeness (bb): 95.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.1 % (506 of 609)	83.1 % (261 of 314)	80.5 % (194 of 241)	94.4 % (51 of 54)
Backbone	95.7 % (308 of 322)	95.5 % (105 of 110)	95.0 % (153 of 161)	98.0 % (50 of 51)
Sidechain	73.4 % (248 of 338)	76.5 % (156 of 204)	69.5 % (91 of 131)	33.3 % (1 of 3)
Aromatic	39.1 % (18 of 46)	78.3 % (18 of 23)	0.0 % (0 of 22)	0.0 % (0 of 1)
Methyl	79.3 % (46 of 58)	79.3 % (23 of 29)	79.3 % (23 of 29)

1. PHD1 finger of KDM5B

AVDLYVCLLC GSGNDEDRLL LCDGCDDSYH TFCLIPPLHD VPKGDWRCPK CLAQE

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 90% H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	PHD1 finger of KDM5B	[U-13C; U-15N]	0.8 mM
2	Phosphate buffer	natural abundance	50 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 100% D2O

#	Name	Isotope labeling	Concentration
5	PHD1 finger of KDM5B	[U-13C; U-15N]	0.8 mM
6	Phosphate buffer	natural abundance	50 mM
7	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291
³¹P	DSS	methyl protons	na	indirect	0.4048086

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291
³¹P	DSS	methyl protons	na	indirect	0.4048086

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291
³¹P	DSS	methyl protons	na	indirect	0.4048086

Referencing offset: 0.13 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291
³¹P	DSS	methyl protons	na	indirect	0.4048086

Referencing offset: 0.4 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2014-08-03

Citation

The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B
Zhang, Y., Yang, H.R., Guo, X., Rong, N.Y., Song, Y.J., Xu, Y.W., Lan, W.X., Xu, Y.H., Cao, C.Y.
Protein. Cell (2014), 5, 837-850, PubMed 24952722 , DOI 10.1007/s13238-014-0078-4 , Abstract

Related entities 1. PHD1 finger of KDM5B, : 1 : 3 : 4 : 345 entities Detail

Interaction partners 1. PHD1 finger of KDM5B, : 4 interactors Detail

More details for 4 interactors identified by 4 citations

Experiments performed 12 experiments Detail

1 3D_15N-separated_NOESY