BMRB Entry 19230
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19230
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Title: Solution structure of Hdm2 with engineered cyclotide PubMed: 23848581
Deposition date: 2013-05-07 Original release date: 2013-07-29
Authors: Majumder, Subhabrata; Ji, Yanbin; Millard, Melissa; Borra, Radikha; Bi, Tao; Elnagar, Ahmed; Neamati, Nouri; Camarero, Julio
Citation: Ji, Yanbin; Majumder, Subhabrata; Millard, Melissa; Borra, Radhika; Bi, Tao; Elnagar, Ahmed; Neamati, Nouri; Shekhtman, Alexander; Camarero, Julio. "In Vivo Activation of the p53 Tumor Suppressor Pathway by an Engineered Cyclotide." J. Am. Chem. Soc. 135, 11623-11633 (2013).
Assembly members:
Hdm2, polymer, 51 residues, 5291.016 Da.
MCo-PMI, polymer, 83 residues, 9814.753 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):
Hdm2: SGSGASKAPTSFAEYWNLLS
AGGVCPKILQRCRRDSDCPG
ACICRGNGYCG
MCo-PMI: LVRPKPLLLKLLKSVGAQKD
TYTMKEVLFYLGQYIMTKRL
YDEKQQHIVYCSNDLLGDLF
GVPSFSVKEHRKIYTMIYRN
LVV
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 147 |
| 15N chemical shifts | 121 |
| 1H chemical shifts | 581 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Hdm2 | 1 |
| 2 | MCo-PMI | 2 |
Entities:
Entity 1, Hdm2 51 residues - 5291.016 Da.
This is an engineered cyclotide based on MCoTI-I., cyclic-pseudo-peptide
| 1 | SER | GLY | SER | GLY | ALA | SER | LYS | ALA | PRO | THR | ||||
| 2 | SER | PHE | ALA | GLU | TYR | TRP | ASN | LEU | LEU | SER | ||||
| 3 | ALA | GLY | GLY | VAL | CYS | PRO | LYS | ILE | LEU | GLN | ||||
| 4 | ARG | CYS | ARG | ARG | ASP | SER | ASP | CYS | PRO | GLY | ||||
| 5 | ALA | CYS | ILE | CYS | ARG | GLY | ASN | GLY | TYR | CYS | ||||
| 6 | GLY |
Entity 2, MCo-PMI 83 residues - 9814.753 Da.
| 1 | LEU | VAL | ARG | PRO | LYS | PRO | LEU | LEU | LEU | LYS | ||||
| 2 | LEU | LEU | LYS | SER | VAL | GLY | ALA | GLN | LYS | ASP | ||||
| 3 | THR | TYR | THR | MET | LYS | GLU | VAL | LEU | PHE | TYR | ||||
| 4 | LEU | GLY | GLN | TYR | ILE | MET | THR | LYS | ARG | LEU | ||||
| 5 | TYR | ASP | GLU | LYS | GLN | GLN | HIS | ILE | VAL | TYR | ||||
| 6 | CYS | SER | ASN | ASP | LEU | LEU | GLY | ASP | LEU | PHE | ||||
| 7 | GLY | VAL | PRO | SER | PHE | SER | VAL | LYS | GLU | HIS | ||||
| 8 | ARG | LYS | ILE | TYR | THR | MET | ILE | TYR | ARG | ASN | ||||
| 9 | LEU | VAL | VAL |
Samples:
sample_1: MCo-PMI 0.2 mM; Hdm2, [U-99% 13C; U-99% 15N], 0.2 mM; H2O 90%; D2O 10%
sample_2: MCo-PMI, [U-99% 15N], 0.2 mM; Hdm2 0.2 mM; H2O 90%; D2O 10%
Sample_3: MCo-PMI 0.2 mM; Hdm2 0.2 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.133 M; pH: 6.5; pressure: 1 atm; temperature: 300 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | Sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
CHRMM v36, CHARMM-Karplus M. - refinement
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
NMR spectrometers:
- Bruker Avance 700 MHz
Related Database Links:
| PDB | |
| BMRB | 15945 18755 2410 6612 |
| DBJ | BAB11975 BAC78209 BAF83030 BAJ17752 |
| EMBL | CAA78055 CAD23251 CAD36959 CAH89564 CAP16708 |
| GB | AAA60568 AAF28866 AAF67833 AAG42840 AAG42841 |
| PRF | 1814460A |
| REF | NP_001003103 NP_001009346 NP_001092577 NP_001098773 NP_001124685 |
| SP | P56950 P56951 Q00987 Q7YRZ8 |
| TPG | DAA29805 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts