BMRB Entry 25829
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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/BMR25829
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Title: p75NTR DD:RhoGDI PubMed: 26646181
Deposition date: 2015-09-30 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_1, polymer, 94 residues, 10172.424 Da.
entity_2, polymer, 174 residues, 19884.719 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: GLYSSLPPAKREEVEKLLNG
SAGDTWRHLAGELGYQPEHI
DSFTHEACPVRALLASWATQ
DSATLDALLAALRRIQRADL
VESLCSESTATSPV
entity_2: AQKSIQEIQELDKDDESLRK
YKEALLGRVAVSADPNVPNV
VVTGLTLVCSSAPGPLELDL
TGDLESFKKQSFVLKEGVEY
RIKISFRVNREIVSGMKYIQ
HTYRKGVKIDKTDYMVGSYG
PRAEEYEFLTPVEEAPKGML
ARGSYSIKSRFTDDDKTDHL
SWEWNLTIKKDWKD
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 878 |
| 15N chemical shifts | 257 |
| 1H chemical shifts | 1713 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
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 |
Entity 2, entity_2 174 residues - 19884.719 Da.
| 1 | ALA | GLN | LYS | SER | ILE | GLN | GLU | ILE | GLN | GLU | ||||
| 2 | LEU | ASP | LYS | ASP | ASP | GLU | SER | LEU | ARG | LYS | ||||
| 3 | TYR | LYS | GLU | ALA | LEU | LEU | GLY | ARG | VAL | ALA | ||||
| 4 | VAL | SER | ALA | ASP | PRO | ASN | VAL | PRO | ASN | VAL | ||||
| 5 | VAL | VAL | THR | GLY | LEU | THR | LEU | VAL | CYS | SER | ||||
| 6 | SER | ALA | PRO | GLY | PRO | LEU | GLU | LEU | ASP | LEU | ||||
| 7 | THR | GLY | ASP | LEU | GLU | SER | PHE | LYS | LYS | GLN | ||||
| 8 | SER | PHE | VAL | LEU | LYS | GLU | GLY | VAL | GLU | TYR | ||||
| 9 | ARG | ILE | LYS | ILE | SER | PHE | ARG | VAL | ASN | ARG | ||||
| 10 | GLU | ILE | VAL | SER | GLY | MET | LYS | TYR | ILE | GLN | ||||
| 11 | HIS | THR | TYR | ARG | LYS | GLY | VAL | LYS | ILE | ASP | ||||
| 12 | LYS | THR | ASP | TYR | MET | VAL | GLY | SER | TYR | GLY | ||||
| 13 | PRO | ARG | ALA | GLU | GLU | TYR | GLU | PHE | LEU | THR | ||||
| 14 | PRO | VAL | GLU | GLU | ALA | PRO | LYS | GLY | MET | LEU | ||||
| 15 | ALA | ARG | GLY | SER | TYR | SER | ILE | LYS | SER | ARG | ||||
| 16 | PHE | THR | ASP | ASP | ASP | LYS | THR | ASP | HIS | LEU | ||||
| 17 | SER | TRP | GLU | TRP | ASN | LEU | THR | ILE | LYS | LYS | ||||
| 18 | ASP | TRP | LYS | ASP |
Samples:
sample_1: p75NTR DD, [U-99% 13C; U-99% 15N], 0.5 mM; DTT, [U-98% 2H], 1 mM; HEPES, [U-98% 2H], 10 mM; EDTA 1 mM; sodium azide 1 mM; RhoGDI 2 mM
sample_2: RhoGDI, [U-99% 13C; U-99% 15N], 0.5 mM; p75NTR DD 2 mM; DTT, [U-98% 2H], 1 mM; HEPES, [U-98% 2H], 10 mM; EDTA 1 mM; sodium azide 1 mM
sample_conditions_1: ionic strength: 10 mM; 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 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 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 13C,15N-filtered NOESY | sample_2 | isotropic | sample_conditions_1 |
| 4D 13C, 15N-edited NOESY | sample_2 | 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