BMRB Entry 17378
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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/BMR17378
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Title: Structure of CEL-PEP-RAGE V domain complex PubMed: 21565706
Deposition date: 2010-12-23 Original release date: 2011-05-18
Authors: Xue, Jing; Rai, Vivek; Schmidt, Ann-Marie; Frolov, Sergey; Reverdatto, Sergey; Singer, David; Chabierski, Stefan; Xie, Jingjing; Burz, David; Shekhtman, Alexander; Hoffman, Ralf
Citation: Xue, Jing; Rai, Vivek; Singer, David; Chabierski, Stefan; Xie, Jingjing; Reverdatto, Sergey; Burz, David; Schmidt, Ann Marie; Hoffmann, Ralf; Shekhtman, Alexander. "Advanced Glycation End Product Recognition by the Receptor for AGEs." Structure 19, 722-732 (2011).
Assembly members:
V_domain, polymer, 105 residues, 11571.429 Da.
CEL-PEP, polymer, 7 residues, 724.677 Da.
MCL, polymer, . residues, 218.250 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):
V_domain: GSAQNITARIGEPLVLKCKG
APKKPPQRLEWKLNTGRTEA
WKVLSPQGGGPWDSVARVLP
NGSLFLPAVGIQDEGIFRCQ
AMNRNGKETKSNYRVRVYQI
PGKPE
CEL-PEP: DEFXADE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 345 |
| 15N chemical shifts | 92 |
| 1H chemical shifts | 656 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | v_domain | 1 |
| 2 | CEL-PEP | 2 |
| 3 | 4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE | 3 |
Entities:
Entity 1, v_domain 105 residues - 11571.429 Da.
Residues 1-2 represent non-native affinity tag Residues 3-105 in the PDB file represent residues 23-123 of the V domain of RAGE.
| 1 | GLY | SER | ALA | GLN | ASN | ILE | THR | ALA | ARG | ILE | ||||
| 2 | GLY | GLU | PRO | LEU | VAL | LEU | LYS | CYS | LYS | GLY | ||||
| 3 | ALA | PRO | LYS | LYS | PRO | PRO | GLN | ARG | LEU | GLU | ||||
| 4 | TRP | LYS | LEU | ASN | THR | GLY | ARG | THR | GLU | ALA | ||||
| 5 | TRP | LYS | VAL | LEU | SER | PRO | GLN | GLY | GLY | GLY | ||||
| 6 | PRO | TRP | ASP | SER | VAL | ALA | ARG | VAL | LEU | PRO | ||||
| 7 | ASN | GLY | SER | LEU | PHE | LEU | PRO | ALA | VAL | GLY | ||||
| 8 | ILE | GLN | ASP | GLU | GLY | ILE | PHE | ARG | CYS | GLN | ||||
| 9 | ALA | MET | ASN | ARG | ASN | GLY | LYS | GLU | THR | LYS | ||||
| 10 | SER | ASN | TYR | ARG | VAL | ARG | VAL | TYR | GLN | ILE | ||||
| 11 | PRO | GLY | LYS | PRO | GLU |
Entity 2, CEL-PEP 7 residues - 724.677 Da.
This sequence contains a modified lysine, Nepsilon -carboxy-ethyl-lysine (CEL). The CEL is denoted by X.
| 1 | ASP | GLU | PHE | CEL | ALA | ASP | GLU |
Entity 3, 4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE - 218.250 Da.
| 1 | MCL |
Samples:
sample_1: V domain, [U-100% 13C; U-100% 15N], 0.1 mM; CEL-PEP 0.3 mM; H2O 90%; D2O 10%
sample-2: V domain, [U-100% 13C; U-100% 15N], 0.32 mM; CEL-PEP 1 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.130 M; pH: 6.5; 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 HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample-2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample-2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample-2 | isotropic | sample_conditions_1 |
Software:
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
CARA, Bartels et al. - chemical shift assignment
NMR spectrometers:
- Bruker Avance 700 MHz
- Bruker Avance 500 MHz
Related Database Links:
| BMRB | 19739 19953 |
| PDB | |
| DBJ | BAA05958 BAA89369 BAC65465 BAG35995 BAG60385 |
| GB | AAA03574 AAB47491 AAH20669 AAX07272 AAX07273 |
| REF | NP_001127 NP_001192046 NP_001193858 NP_001193863 NP_001193865 |
| SP | Q15109 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts