BMRB: 16865

Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing N-terminal acetylation at serine 1

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 serine 1 (polymer, Thiol state: not present), 20 monomers, 2034.333 Da Detail

XGRGKGGKGL GKGGAKRHRK

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. ACS (non-polymer, Thiol state: not present), 395.452 Da
4. ZN (non-polymer, Thiol state: not present), 65.409 × 4 Da

Total weight

15424.781 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: 98.5 %, Completeness: 81.0 %, Completeness (bb): 77.0 % Detail

Download

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

Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	81.0 % (1203 of 1486)	89.1 % (696 of 781)	68.4 % (388 of 567)	86.2 % (119 of 138)
Backbone	77.0 % (605 of 786)	93.5 % (259 of 277)	62.3 % (238 of 382)	85.0 % (108 of 127)
Sidechain	86.4 % (705 of 816)	86.7 % (437 of 504)	85.4 % (257 of 301)	100.0 % (11 of 11)
Aromatic	77.2 % (88 of 114)	78.9 % (45 of 57)	74.1 % (40 of 54)	100.0 % (3 of 3)
Methyl	95.5 % (84 of 88)	97.7 % (43 of 44)	93.2 % (41 of 44)

1. histone H4 acet serine 1

XGRGKGGKGL GKGGAKRHRK

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: -0.7 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	water	methyl carbons	42.0 ppm	internal	direct	1.0
1H	water	methyl protons	4.73 ppm	internal	direct	1.0
15N	water	nitrogen	118.0 ppm	internal	direct	1.0

Hide chemical shift referencing parameters

LACS Plot; CB

Referencing offset: -0.7 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	water	methyl carbons	42.0 ppm	internal	direct	1.0
1H	water	methyl protons	4.73 ppm	internal	direct	1.0
15N	water	nitrogen	118.0 ppm	internal	direct	1.0

Hide chemical shift referencing parameters

LACS Plot; HA

Referencing offset: 0.07 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	water	methyl carbons	42.0 ppm	internal	direct	1.0
1H	water	methyl protons	4.73 ppm	internal	direct	1.0
15N	water	nitrogen	118.0 ppm	internal	direct	1.0

Hide chemical shift referencing parameters

Protein Blocks Logo

Calculated from 20 models in PDB: 2KWO, 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 serine 1, : 51 : 1 entities Detail

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

Interaction partners 1. histone H4 acet serine 1, : 229 interactors Detail

Experiments performed 5 experiments Detail