BMRB Entry 18439
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18439
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Title: solution structures of BRD4 second bromodomain with NF-kB-K310ac peptide PubMed: 22645123
Deposition date: 2012-05-03 Original release date: 2012-06-05
Authors: Zhang, Guangtao; Liu, Ruijie; Zhong, Yifei; Plotnikov, Alexander; Zhang, Weijia; Rusinova, Elena; Gerona-Nevarro, Guillermo; Moshkina, Natasha; Joshua, Jennifer; Chuang, Peter; Ohlmeyer, Michael; He, John Cijiang
Citation: Zhang, Guangtao; Liu, Ruijie; Zhong, Yifei; Plotnikov, Alexander; Zhang, Weijia; Zeng, Lei; Rusinova, Elena; Gerona-Nevarro, Guillermo; Moshkina, Natasha; Joshua, Jennifer; Chuang, Peter; Ohlmeyer, Michael; He, John Cijiang; Zhou, Ming-Ming. "Down-regulation of NF-B transcriptional activity in HIV-associated kidney disease by BRD4 inhibition." J. Biol. Chem. 287, 28840-28851 (2012).
Assembly members:
entity_1, polymer, 13 residues, 1663.968 Da.
entity_2, polymer, 128 residues, 14842.159 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):
entity_1: RTYETFXSIMKKS
entity_2: KDVPDSQQHPAPEKSSKVSE
QLKCCSGILKEMFAKKHAAY
AWPFYKPVDVEALGLHDYCD
IIKHPMDMSTIKSKLEAREY
RDAQEFGADVRLMFSNCYKY
NPPDHEVVAMARKLQDVFEM
RFAKMPDE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 444 |
| 15N chemical shifts | 117 |
| 1H chemical shifts | 874 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | NF-kB-K310ac peptide | 1 |
| 2 | BRD4 second bromodomain | 2 |
Entities:
Entity 1, NF-kB-K310ac peptide 13 residues - 1663.968 Da.
| 1 | ARG | THR | TYR | GLU | THR | PHE | ALY | SER | ILE | MET | ||||
| 2 | LYS | LYS | SER |
Entity 2, BRD4 second bromodomain 128 residues - 14842.159 Da.
| 1 | LYS | ASP | VAL | PRO | ASP | SER | GLN | GLN | HIS | PRO | ||||
| 2 | ALA | PRO | GLU | LYS | SER | SER | LYS | VAL | SER | GLU | ||||
| 3 | GLN | LEU | LYS | CYS | CYS | SER | GLY | ILE | LEU | LYS | ||||
| 4 | GLU | MET | PHE | ALA | LYS | LYS | HIS | ALA | ALA | TYR | ||||
| 5 | ALA | TRP | PRO | PHE | TYR | LYS | PRO | VAL | ASP | VAL | ||||
| 6 | GLU | ALA | LEU | GLY | LEU | HIS | ASP | TYR | CYS | ASP | ||||
| 7 | ILE | ILE | LYS | HIS | PRO | MET | ASP | MET | SER | THR | ||||
| 8 | ILE | LYS | SER | LYS | LEU | GLU | ALA | ARG | GLU | TYR | ||||
| 9 | ARG | ASP | ALA | GLN | GLU | PHE | GLY | ALA | ASP | VAL | ||||
| 10 | ARG | LEU | MET | PHE | SER | ASN | CYS | TYR | LYS | TYR | ||||
| 11 | ASN | PRO | PRO | ASP | HIS | GLU | VAL | VAL | ALA | MET | ||||
| 12 | ALA | ARG | LYS | LEU | GLN | ASP | VAL | PHE | GLU | MET | ||||
| 13 | ARG | PHE | ALA | LYS | MET | PRO | ASP | GLU |
Samples:
sample_2: sodium phosphate 100 mM; DTT, [U-100% 2H], 5 mM; D2O 10%; H2O 90%
sample_1: sodium phosphate 100 mM; DTT, [U-100% 2H], 5 mM; D2O 100%
sample_conditions_1: ionic strength: 100 mM; 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(CO)CACB | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 13C-Edited-15N/13C filtered NOESY | sample_1 | isotropic | sample_conditions_1 |
Software:
ARIA v2.3, Linge, O'Donoghue and Nilges - refinement
NMRPipe v7.1, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift calculation, processing
TALOS v3.70F1, Cornilescu, Delaglio and Bax - geometry optimization
NMRView v5.04, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking
CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 900 MHz
- Bruker Avance 600 MHz
- Bruker DRX 500 MHz
Related Database Links:
| BMRB | 15057 19738 |
| PDB | |
| REF | XP_004761195 XP_006524755 XP_006524756 XP_008763395 |
Download simulated HSQC data in one of the following formats:
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SPARKY: Backbone
or all simulated shifts