BMRB Entry 25883
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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/BMR25883
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Title: DD homodimer PubMed: 26646181
Deposition date: 2015-11-07 Original release date: 2015-12-21
Authors: Lin, Zhi; Ibanez, Carlos
Citation: Lin, Zhi; Tann, Jason; Goh, Eddy; Kelly, Claire; Lim, Kim; Gao, Jian; Ibanez, Carlos. "Structural basis of death domain signaling in the p75 neurotrophin receptor" Elife 4, 11692-11692 (2015).
Assembly members:
entity, polymer, 94 residues, 10172.424 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: GLYSSLPPAKREEVEKLLNG
SAGDTWRHLAGELGYQPEHI
DSFTHEACPVRALLASWATQ
DSATLDALLAALRRIQRADL
VESLCSESTATSPV
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 284 |
| 15N chemical shifts | 96 |
| 1H chemical shifts | 589 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 1 |
Entities:
Entity 1, entity_1 94 residues - 10172.424 Da.
| 1 | GLY | LEU | TYR | SER | SER | LEU | PRO | PRO | ALA | LYS | ||||
| 2 | ARG | GLU | GLU | VAL | GLU | LYS | LEU | LEU | ASN | GLY | ||||
| 3 | SER | ALA | GLY | ASP | THR | TRP | ARG | HIS | LEU | ALA | ||||
| 4 | GLY | GLU | LEU | GLY | TYR | GLN | PRO | GLU | HIS | ILE | ||||
| 5 | ASP | SER | PHE | THR | HIS | GLU | ALA | CYS | PRO | VAL | ||||
| 6 | ARG | ALA | LEU | LEU | ALA | SER | TRP | ALA | THR | GLN | ||||
| 7 | ASP | SER | ALA | THR | LEU | ASP | ALA | LEU | LEU | ALA | ||||
| 8 | ALA | LEU | ARG | ARG | ILE | GLN | ARG | ALA | ASP | LEU | ||||
| 9 | VAL | GLU | SER | LEU | CYS | SER | GLU | SER | THR | ALA | ||||
| 10 | THR | SER | PRO | VAL |
Samples:
sample_1: p75NTR DD, [U-99% 13C; U-99% 15N], 1 mM; DTT, [U-98% 2H], 10 mM; p75NTR DD 1 mM; sodium phosphate 50 mM; H2O 95%; D2O 5%
sample_conditions_1: pH: 6.9; pressure: 1 atm; temperature: 273 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 13C,15N-filtered NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 13C, 15N-edited NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | 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 HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 13C,15N-filtered NOESY | sample_1 | isotropic | sample_conditions_1 |
| 4D 13C, 15N-edited NOESY | sample_1 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView, Johnson, One Moon Scientific - data analysis
CYANA, Guntert, Braun and Wuthrich - structure solution
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
NMR spectrometers:
- Bruker Avance 800 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts