BMRB Entry 17780
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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/BMR17780
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Title: Human prion protein with E219K protective polymorphism PubMed: 22676969
Deposition date: 2011-07-14 Original release date: 2012-06-25
Authors: Biljan, Ivana; Ilc, Gregor; Giancin, Gabriele; Zhukov, Igor; Plavec, Janez; Legname, Guiseppe
Citation: Biljan, Ivana; Giachin, Gabriele; Ilc, Gregor; Zhukov, Igor; Plavec, Janez; Legname, Giuseppe. "Structural basis for the protective effect of the human prion protein carrying the dominant-negative E219K polymorphism." Biochem. J. 446, 243-251 (2012).
Assembly members:
Hpp_E219K, polymer, 142 residues, 16169.169 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):
Hpp_E219K: GQGGGTHSQWNKPSKPKTNM
KHMAGAAAAGAVVGGLGGYM
LGSAMSRPIIHFGSDYEDRY
YRENMHRYPNQVYYRPMDEY
SNQNNFVHDCVNITIKQHTV
TTTTKGENFTETDVKMMERV
VEQMCITQYKRESQAYYQRG
SS
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 461 |
| 15N chemical shifts | 148 |
| 1H chemical shifts | 1281 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Human prion protein with E219K protective polymorphism | 1 |
Entities:
Entity 1, Human prion protein with E219K protective polymorphism 142 residues - 16169.169 Da.
| 1 | GLY | GLN | GLY | GLY | GLY | THR | HIS | SER | GLN | TRP | ||||
| 2 | ASN | LYS | PRO | SER | LYS | PRO | LYS | THR | ASN | MET | ||||
| 3 | LYS | HIS | MET | ALA | GLY | ALA | ALA | ALA | ALA | GLY | ||||
| 4 | ALA | VAL | VAL | GLY | GLY | LEU | GLY | GLY | TYR | MET | ||||
| 5 | LEU | GLY | SER | ALA | MET | SER | ARG | PRO | ILE | ILE | ||||
| 6 | HIS | PHE | GLY | SER | ASP | TYR | GLU | ASP | ARG | TYR | ||||
| 7 | TYR | ARG | GLU | ASN | MET | HIS | ARG | TYR | PRO | ASN | ||||
| 8 | GLN | VAL | TYR | TYR | ARG | PRO | MET | ASP | GLU | TYR | ||||
| 9 | SER | ASN | GLN | ASN | ASN | PHE | VAL | HIS | ASP | CYS | ||||
| 10 | VAL | ASN | ILE | THR | ILE | LYS | GLN | HIS | THR | VAL | ||||
| 11 | THR | THR | THR | THR | LYS | GLY | GLU | ASN | PHE | THR | ||||
| 12 | GLU | THR | ASP | VAL | LYS | MET | MET | GLU | ARG | VAL | ||||
| 13 | VAL | GLU | GLN | MET | CYS | ILE | THR | GLN | TYR | LYS | ||||
| 14 | ARG | GLU | SER | GLN | ALA | TYR | TYR | GLN | ARG | GLY | ||||
| 15 | SER | SER |
Samples:
sample_1: Hpp_E219K, [U-100% 13C; U-100% 15N], 1.5 mM; H2O 90%; D2O 10%; buffer sodium acetate-d3 20 mM; NaCl 0.1 M
sample_2: Hpp_E219K, [U-100% 13C; U-100% 15N], 1.5 mM; D2O 100%; buffer sodium acetate-d3 20 mM; NaCl 0.1 M
sample_conditions_1: ionic strength: 0.1 M; pH: 5.5; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 0.1 M; pD: 5.9; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_2 |
| 3D 1H-13C NOESY aliphatic | sample_2 | isotropic | sample_conditions_2 |
| 3D 1H-13C NOESY aromatic | sample_2 | isotropic | sample_conditions_2 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - data analysis
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
YASARA, (YASARA) - refinement
NMR spectrometers:
- Varian Uniform NMR System 800 MHz
Related Database Links:
| BMRB | 15676 16743 16757 17714 17756 17757 18426 18550 19268 4379 4402 4434 4620 4641 4736 |
| PDB | |
| DBJ | BAA00011 BAF62360 BAG32276 BAG32277 BAG32278 |
| EMBL | CAA58442 CAG46836 CAG46869 |
| GB | AAA19664 AAA60182 AAA68632 AAA68633 AAB59442 |
| REF | NP_000302 NP_001009093 NP_001073590 NP_001073591 NP_001073592 |
| SP | P04156 P40252 P61766 P61767 P61768 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts