BMRB: 16861

Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing acetylation at lysine 16

Authors

Zeng, L., Zhang, Q., Li, S., Plotnikov, A.N., Walsh, M.J., ZHOU, M.

Assembly

Tandem PHD finger of Human DPF3b

Entity

1. histone H4 acet lys 16 (polymer, Thiol state: not present), 15 monomers, 1674.994 Da Detail

GLGKGGAXRH RKVLR

2. double PHD fingers (polymer, Thiol state: free and other bound), 114 monomers, 12733.36 Da Detail

GSYCDFCLGG SNMNKKSGRP EELVSCADCG RSGHPTCLQF TLNMTEAVKT YKWQCIECKS CILCGTSEND DQLLFCDDCD RGYHMYCLNP PVAEPPEGSW SCHLCWELLK EKAS

3. ZN (non-polymer, Thiol state: not present), 65.409 × 4 Da

Total weight

14669.99 Da

Max. entity weight

12733.36 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 82.0 %, Completeness (bb): 77.6 % Detail

Download

• NMR-STAR v3.1 (partial)
• BMRB/XML (partial)
• CSV
• TSV

Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	82.0 % (1178 of 1436)	91.2 % (685 of 751)	67.9 % (375 of 552)	88.7 % (118 of 133)
Backbone	77.6 % (587 of 756)	96.2 % (253 of 263)	61.2 % (227 of 371)	87.7 % (107 of 122)
Sidechain	87.4 % (695 of 795)	88.5 % (432 of 488)	85.1 % (252 of 296)	100.0 % (11 of 11)
Aromatic	78.9 % (90 of 114)	80.7 % (46 of 57)	75.9 % (41 of 54)	100.0 % (3 of 3)
Methyl	90.6 % (87 of 96)	95.8 % (46 of 48)	85.4 % (41 of 48)

1. histone H4 acet lys 16

GLGKGGAXRH RKVLR

2. double PHD fingers

GSYCDFCLGG SNMNKKSGRP EELVSCADCG RSGHPTCLQF TLNMTEAVKT YKWQCIECKS CILCGTSEND DQLLFCDDCD RGYHMYCLNP PVAEPPEGSW SCHLCWELLK EKAS

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		100 mM
2	DTT	natural abundance		2 mM
3	D2O	natural abundance		100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
4	sodium phosphate	natural abundance		100 mM
5	DTT	natural abundance		2 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Hide sample codition

LACS Plot; CA

Referencing offset: -0.75 ppm, Outliers: 3 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	na	na	0.0 ppm	null	null	0.0
1H	na	na	0.0 ppm	null	null	0.0
15N	na	na	0.0 ppm	null	null	0.0

Hide chemical shift referencing parameters

LACS Plot; CB

Referencing offset: -0.75 ppm, Outliers: 3 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	na	na	0.0 ppm	null	null	0.0
1H	na	na	0.0 ppm	null	null	0.0
15N	na	na	0.0 ppm	null	null	0.0

Hide chemical shift referencing parameters

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	na	na	0.0 ppm	null	null	0.0
1H	na	na	0.0 ppm	null	null	0.0
15N	na	na	0.0 ppm	null	null	0.0

Hide chemical shift referencing parameters

Protein Blocks Logo

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

---

Release date

2010-09-02

Citation

Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b
Zeng, L., Zhang, Q., Li, S., Plotnikov, A.N., Walsh, M.J., ZHOU, M.
Nature (2010), 466, 258-262, PubMed 20613843 , DOI 10.1038/nature09139 , Abstract

Related entities 1. histone H4 acet lys 16, : 1 : 3 entities Detail

Related entities 2. double PHD fingers, : 1 : 3 : 54 entities Detail

Experiments performed 5 experiments Detail