BMRB Entry 17071
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR17071
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Title: Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide PubMed: 21047797
Deposition date: 2010-07-22 Original release date: 2010-08-18
Authors: Kaustov, Lilia; Lemak, Alexander; Fares, Christophe; Gutmanas, Aleksandras; Quang, Hui; Loppnau, Peter; Min, Jinrong; Edwards, Al; Arrowsmith, Cheryl
Citation: Kaustov, Lilia; Ouyang, Hui; Amaya, Maria; Lemak, Alexander; Nady, Nataliya; Duan, Shili; Wasney, Gregory; Li, Zhihong; Vedadi, Masoud; Schapira, Matthieu; Min, Jinrong; Arrowsmith, Cheryl. "Recognition and specificity determinants of the human cbx chromodomains." J. Biol. Chem. 286, 521-529 (2011).
Assembly members:
Cbx3, polymer, 54 residues, 6354.158 Da.
H3K9me3, polymer, 15 residues, 1607.892 Da.
Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Cbx3: GEFVVEKVLDRRVVNGKVEY
FLKWKGFTDADNTWEPEENL
DCPELIEAFLNSQK
H3K9me3: ARTKQTARXSTGGKA
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 241 |
| 15N chemical shifts | 56 |
| 1H chemical shifts | 424 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Cbx3 | 1 |
| 2 | H3K9me3 | 2 |
Entities:
Entity 1, Cbx3 54 residues - 6354.158 Da.
| 1 | GLY | GLU | PHE | VAL | VAL | GLU | LYS | VAL | LEU | ASP | ||||
| 2 | ARG | ARG | VAL | VAL | ASN | GLY | LYS | VAL | GLU | TYR | ||||
| 3 | PHE | LEU | LYS | TRP | LYS | GLY | PHE | THR | ASP | ALA | ||||
| 4 | ASP | ASN | THR | TRP | GLU | PRO | GLU | GLU | ASN | LEU | ||||
| 5 | ASP | CYS | PRO | GLU | LEU | ILE | GLU | ALA | PHE | LEU | ||||
| 6 | ASN | SER | GLN | LYS |
Entity 2, H3K9me3 15 residues - 1607.892 Da.
X = N-TRIMETHYLLYSINE
| 1 | ALA | ARG | THR | LYS | GLN | THR | ALA | ARG | M3L | SER | ||||
| 2 | THR | GLY | GLY | LYS | ALA |
Samples:
sample_1: Cbx3, [U-13C; U-15N], 0.43 mM; H3K9me3 1.2 mM; sodium phosphate 20 mM; sodium chloride 200 mM; DTT 2 mM; TCEP 1 mM; PMSF 0.5 mM; Benzamidine 1 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 200 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D-15N-NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D-13C-NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D -13C-aromatic-NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 13C/15N-filtered/edited NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D aro 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D-aromatic 1H-13C-TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
ABACUS, Grishaev - chemical shift assignment
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - peak picking
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
NMR spectrometers:
- Bruker Avance 800 MHz
- Varian INOVA 500 MHz
Related Database Links:
| PDB | |
| DBJ | BAA33401 BAA83340 BAB22450 BAC39078 BAE27125 |
| EMBL | CAA40012 CAC42944 CAH92483 |
| GB | AAB48101 AAF62370 AAH00954 AAH18354 AAH59831 |
| REF | NP_001008314 NP_001094668 NP_001126464 NP_001180536 NP_001233631 |
| SP | P23198 Q13185 Q5R6X7 |
| TPG | DAA30517 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts