BMRB Entry 18709
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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/BMR18709
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Title: HMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transactivation domain interaction and is regulated by the acidic tail PubMed: 23063560
Deposition date: 2012-09-12 Original release date: 2012-10-29
Authors: Rowell, John; Simpson, Kathryn; Stott, Katherine; Watson, Matthew; Thomas, Jean
Citation: Rowell, John; Simpson, Kathryn; Stott, Katherine; Watson, Matthew; Thomas, Jean. "HMGB1-facilitated p53 DNA binding occurs via HMG-Box/p53 transactivation domain interaction, regulated by the acidic tail." Structure 20, 2014-2024 (2012).
Assembly members:
entity_1, polymer, 83 residues, 9705.259 Da.
entity_2, polymer, 93 residues, 9979.1 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):
entity_1: GKGDPKKPRGKMSSYAFFVQ
TCREEHKKKHPDASVNFSEF
SKKCSERWKTMSAKEKGKFE
DMAKADKARYEREMKTYIPP
KGE
entity_2: MEEPQSDPSVEPPLSQETFS
DLWKLLPENNVLSPLPSQAM
DDLMLSPDDIEQWFTEDPGP
DEAPRMPEAAPPVAPAPAAP
TPAAPAPAPSWPL
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 749 |
| 15N chemical shifts | 159 |
| 1H chemical shifts | 1172 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | abox | 1 |
| 2 | p53 | 2 |
Entities:
Entity 1, abox 83 residues - 9705.259 Da.
| 1 | GLY | LYS | GLY | ASP | PRO | LYS | LYS | PRO | ARG | GLY | ||||
| 2 | LYS | MET | SER | SER | TYR | ALA | PHE | PHE | VAL | GLN | ||||
| 3 | THR | CYS | ARG | GLU | GLU | HIS | LYS | LYS | LYS | HIS | ||||
| 4 | PRO | ASP | ALA | SER | VAL | ASN | PHE | SER | GLU | PHE | ||||
| 5 | SER | LYS | LYS | CYS | SER | GLU | ARG | TRP | LYS | THR | ||||
| 6 | MET | SER | ALA | LYS | GLU | LYS | GLY | LYS | PHE | GLU | ||||
| 7 | ASP | MET | ALA | LYS | ALA | ASP | LYS | ALA | ARG | TYR | ||||
| 8 | GLU | ARG | GLU | MET | LYS | THR | TYR | ILE | PRO | PRO | ||||
| 9 | LYS | GLY | GLU |
Entity 2, p53 93 residues - 9979.1 Da.
| 1 | MET | GLU | GLU | PRO | GLN | SER | ASP | PRO | SER | VAL | ||||
| 2 | GLU | PRO | PRO | LEU | SER | GLN | GLU | THR | PHE | SER | ||||
| 3 | ASP | LEU | TRP | LYS | LEU | LEU | PRO | GLU | ASN | ASN | ||||
| 4 | VAL | LEU | SER | PRO | LEU | PRO | SER | GLN | ALA | MET | ||||
| 5 | ASP | ASP | LEU | MET | LEU | SER | PRO | ASP | ASP | ILE | ||||
| 6 | GLU | GLN | TRP | PHE | THR | GLU | ASP | PRO | GLY | PRO | ||||
| 7 | ASP | GLU | ALA | PRO | ARG | MET | PRO | GLU | ALA | ALA | ||||
| 8 | PRO | PRO | VAL | ALA | PRO | ALA | PRO | ALA | ALA | PRO | ||||
| 9 | THR | PRO | ALA | ALA | PRO | ALA | PRO | ALA | PRO | SER | ||||
| 10 | TRP | PRO | LEU |
Samples:
sample_1: entity_10.1 – 1 mM; entity_20.1 – 1 mM; sodium phosphate 10 mM; EDTA 1 mM; DTT 1 mM; PMSF 0.5 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.01 M; pH: 7.0; 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 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY, X-filteref | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
Software:
AZARA, Boucher - processing
ARIA, CCPN - structure solution
Analysis, CCPN - chemical shift assignment
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
NMR spectrometers:
- Bruker DRX 800 MHz
- Bruker DRX 500 MHz
Related Database Links:
| BMRB | 11147 11532 15148 15149 15502 4079 17073 17760 |
| PDB | |
| DBJ | BAA09924 BAC29902 BAC34367 BAC34773 BAC38678 BAC16799 BAG35463 BAG64357 BAI45431 BAJ52715 |
| EMBL | CAA31110 CAA31284 CAA56631 CAA68441 CAA68526 CAA26306 CAA38095 CAA42625 CAA42626 CAA42627 |
| GB | AAA20508 AAA31050 AAA40729 AAA57042 AAA64970 AAA59987 AAA59988 AAA59989 AAA61211 AAA61212 |
| PIR | S29857 |
| REF | NP_001002937 NP_001004034 NP_001075304 NP_001102843 NP_001162380 NP_000537 NP_001119584 NP_001119585 NP_001119586 NP_001119590 |
| SP | A9RA84 B0CM99 B1MTB0 P07156 P09429 P04637 Q9TTA1 |
| TPG | DAA21468 DAA23902 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts