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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: 99.3 %, Completeness: 80.7 %, Completeness (bb): 76.9 % Detail

Polymer type: polypeptide(L)

Total1H13C15N
All80.7 % (1204 of 1492)90.7 % (708 of 781)66.3 % (376 of 567)83.3 % (120 of 144)
Backbone76.9 % (591 of 769)96.9 % (252 of 260)60.2 % (230 of 382)85.8 % (109 of 127)
Sidechain85.7 % (719 of 839)87.5 % (456 of 521)83.7 % (252 of 301)64.7 % (11 of 17)
Aromatic75.4 % (86 of 114)77.2 % (44 of 57)72.2 % (39 of 54)100.0 % (3 of 3)
Methyl96.6 % (85 of 88)100.0 % (44 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

Sample #1

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


#NameIsotope labelingTypeConcentration
1sodium phosphatenatural abundance100 mM
2DTTnatural abundance2 mM
3D2Onatural abundance100 %
Sample #2

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


#NameIsotope labelingTypeConcentration
4sodium phosphatenatural abundance100 mM
5DTTnatural abundance2 mM
6H2Onatural abundance90 %
7D2Onatural abundance10 %

LACS Plot; CA
Referencing offset: -0.7 ppm, Outliers: 3 Detail
LACS Plot; CB
Referencing offset: -0.7 ppm, Outliers: 3 Detail
LACS Plot; HA
Referencing offset: 0.07 ppm, Outliers: 1 Detail
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 ,
Related entities 1. histone H4 acet serine 1, : 133 : 1 entities Detail
Related entities 2. double PHD fingers, : 1 : 3 : 16 entities Detail
Interaction partners 1. histone H4 acet serine 1, : 254 interactors Detail
Experiments performed 5 experiments Detail
Keywords DPF3, H4, Histone, PHD, acetyl-serine