BMRB Entry 16865
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16865
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Title: 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 PubMed: 20613843
Deposition date: 2010-04-14 Original release date: 2010-09-03
Authors: Zeng, Lei; Zhang, Qiang; Li, SiDe; Plotnikov, Alexander; Walsh, Martin; ZHOU, MING-MING
Citation: Zeng, Lei; Zhang, Qiang; Li, SiDe; Plotnikov, Alexander; Walsh, Martin; ZHOU, MING-MING. "Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b" Nature 466, 258-262 (2010).
Assembly members:
histone_H4_acet_serine_1, polymer, 20 residues, 1914.308 Da.
double_PHD_fingers, polymer, 114 residues, 12746.515 Da.
ACS, non-polymer, 395.452 Da.
ZN, non-polymer, 65.409 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
histone_H4_acet_serine_1: XGRGKGGKGLGKGGAKRHRK
double_PHD_fingers: GSYCDFCLGGSNMNKKSGRP
EELVSCADCGRSGHPTCLQF
TLNMTEAVKTYKWQCIECKS
CILCGTSENDDQLLFCDDCD
RGYHMYCLNPPVAEPPEGSW
SCHLCWELLKEKAS
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 364 |
| 15N chemical shifts | 117 |
| 1H chemical shifts | 801 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | histone_H4_acet_serine_1 | 1 |
| 2 | double_PHD_fingerss | 2 |
| 3 | ACS | 3 |
| 4 | ZINC ION_1 | 4 |
| 5 | ZINC ION_2 | 4 |
| 6 | ZINC ION_3 | 4 |
| 7 | ZINC ION_4 | 4 |
Entities:
Entity 1, histone_H4_acet_serine_1 20 residues - 1914.308 Da.
| 1 | SAC | GLY | ARG | GLY | LYS | GLY | GLY | LYS | GLY | LEU | |
| 2 | GLY | LYS | GLY | GLY | ALA | LYS | ARG | HIS | ARG | LYS |
Entity 2, double_PHD_fingerss 114 residues - 12746.515 Da.
| 1 | GLY | SER | TYR | CYS | ASP | PHE | CYS | LEU | GLY | GLY | ||||
| 2 | SER | ASN | MET | ASN | LYS | LYS | SER | GLY | ARG | PRO | ||||
| 3 | GLU | GLU | LEU | VAL | SER | CYS | ALA | ASP | CYS | GLY | ||||
| 4 | ARG | SER | GLY | HIS | PRO | THR | CYS | LEU | GLN | PHE | ||||
| 5 | THR | LEU | ASN | MET | THR | GLU | ALA | VAL | LYS | THR | ||||
| 6 | TYR | LYS | TRP | GLN | CYS | ILE | GLU | CYS | LYS | SER | ||||
| 7 | CYS | ILE | LEU | CYS | GLY | THR | SER | GLU | ASN | ASP | ||||
| 8 | ASP | GLN | LEU | LEU | PHE | CYS | ASP | ASP | CYS | ASP | ||||
| 9 | ARG | GLY | TYR | HIS | MET | TYR | CYS | LEU | ASN | PRO | ||||
| 10 | PRO | VAL | ALA | GLU | PRO | PRO | GLU | GLY | SER | TRP | ||||
| 11 | SER | CYS | HIS | LEU | CYS | TRP | GLU | LEU | LEU | LYS | ||||
| 12 | GLU | LYS | ALA | SER |
Entity 3, ACS - C13 H21 N3 O7 S2 - 395.452 Da.
| 1 | ACS |
Entity 4, ZINC ION_1 - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_1: sodium phosphate 100 mM; DTT 2 mM; D2O 100%
sample_2: sodium phosphate 100 mM; DTT 2 mM; H2O 90%; D2O 10%
sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(COCA)CB | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D_13C-Edited_13C/15N-filtered NOESY | sample_1 | isotropic | sample_conditions_1 |
Software:
ARIA v2.2, Linge, O'Donoghue and Nilges - refinement
NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift calculation, processing
NMRView v5.04, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking
CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution
NMR spectrometers:
- Bruker Avance 900 MHz
- Bruker Avance 800 MHz
- Bruker Avance 600 MHz
- Bruker DRX 500 MHz
Related Database Links:
| PDB | |
| DBJ | BAA19208 BAA21442 BAA85120 BAB08365 BAB09507 BAC30204 |
| EMBL | CAA17818 CAA24130 CAA24373 CAA24645 CAA24924 |
| GB | AAA20820 AAA20821 AAA28606 AAA30002 AAA30024 AAX20019 EDL02734 EGV99590 EHH28015 EHH63746 |
| PIR | D56618 S11312 S21367 S68537 |
| PRF | 0901261A 0912198A 1202262E 1314298A 1707275C |
| REF | NP_001011609 NP_001016869 NP_001027284 NP_001027288 NP_001027293 NP_001254554 NP_001267471 XP_001140541 XP_001254780 XP_001375927 |
| SP | P02309 P04914 P04915 P08436 P09322 P58269 Q92784 |
| TPE | CBF86829 CBF88885 CEL65759 CEL73296 |
| TPG | DAA07130 DAA10515 DAA13862 DAA16108 DAA16158 DAA25179 |
| BMRB | 16858 16859 16861 |
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