BMRB Entry 31034
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31034
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NMR-STAR v3 text file.
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Title: Preligand association structure of DR5 PubMed: 36604598
Deposition date: 2022-07-17 Original release date: 2023-02-09
Authors: Du, G.; Zhao, L.; Chou, J.
Citation: Du, Gang; Zhao, Linlin; Zheng, Yumei; Belfetmi, Anissa; Cai, Tiantian; Xu, Boying; Heyninck, Karen; Van Den Heede, Kim; Buyse, Marie-Ange; Fontana, Pietro; Bowman, Michael; Lin, Lih-Ling; Wu, Hao; Chou, James Jeiwen. "Autoinhibitory structure of preligand association state implicates a new strategy to attain effective DR5 receptor activation" Cell Res. 33, 131-146 (2023).
Assembly members:
entity_1, polymer, 109 residues, 12232.644 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: Komagataella pastoris
Entity Sequences (FASTA):
entity_1: SEGLCPPGHHISEDGRDCIS
CKYGQDYSTHWNDLLFCLRC
TRCDSGEVELSPCTTTRNTV
CQCEEGTFREEDSPEMCRKC
RTGCPRGMVKVGDCTPWSDI
ECVHKESGD
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 348 |
| 15N chemical shifts | 97 |
| 1H chemical shifts | 386 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 1 |
| 3 | unit_3 | 1 |
Entities:
Entity 1, unit_1 109 residues - 12232.644 Da.
| 1 | SER | GLU | GLY | LEU | CYS | PRO | PRO | GLY | HIS | HIS | ||||
| 2 | ILE | SER | GLU | ASP | GLY | ARG | ASP | CYS | ILE | SER | ||||
| 3 | CYS | LYS | TYR | GLY | GLN | ASP | TYR | SER | THR | HIS | ||||
| 4 | TRP | ASN | ASP | LEU | LEU | PHE | CYS | LEU | ARG | CYS | ||||
| 5 | THR | ARG | CYS | ASP | SER | GLY | GLU | VAL | GLU | LEU | ||||
| 6 | SER | PRO | CYS | THR | THR | THR | ARG | ASN | THR | VAL | ||||
| 7 | CYS | GLN | CYS | GLU | GLU | GLY | THR | PHE | ARG | GLU | ||||
| 8 | GLU | ASP | SER | PRO | GLU | MET | CYS | ARG | LYS | CYS | ||||
| 9 | ARG | THR | GLY | CYS | PRO | ARG | GLY | MET | VAL | LYS | ||||
| 10 | VAL | GLY | ASP | CYS | THR | PRO | TRP | SER | ASP | ILE | ||||
| 11 | GLU | CYS | VAL | HIS | LYS | GLU | SER | GLY | ASP |
Samples:
sample_1: DR5 ectodomain, [U-100% 15N, U-100% 13C, U-85% 2H], 400 uM; DGS-NTA (Ni) 4.4 mM; DMPC 44 mM; D7PC 88 mM
sample_2: DR5 ectodomain, [U-100% 15N; U-100% 2H], 500 uM; DGS-NTA (Ni) 5.5 mM; DMPC 55 mM; D7PC 110 mM
sample_3: DR5 ectodomain, [U-100% 13C], 250 uM; DGS-NTA (Ni) 5.5 mM; DMPC 55 mM; D7PC 110 mM; Isotopically mixed DR5 ectodomain, [U-100% 15N; U-100% 2H], 250 uM
sample_4: DR5 ectodomain 250 uM; DGS-NTA (Ni) 5.5 mM; DMPC 55 mM; D7PC 110 mM; Isotopically mixed DR5 ectodomain, [U-100% 13C; U-100% 15N; U-95% 2H], 250 uM
sample_5: DR5 ectodomain, [U-100% 13C; U-100% 15N], 500 uM; DGS-NTA (Ni) 5.5 mM; DMPC 55 mM; D7PC 110 mM
sample_6: DR5 ectodomain, [U-100% 15N, U-85% 2H], 400 uM; DGS-NTA (Ni) 4.4 mM; DMPC 44 mM; D7PC 88 mM
sample_conditions_1: ionic strength: 50 mM; pH: 7.2; pressure: 1 atm; temperature: 310 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N TROSY-HSQC | 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 HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY-TROSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(COCA)CB | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY-TROSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY-TROSY | sample_3 | isotropic | sample_conditions_1 |
| 13C-filtered 1H-15N NOESY-TROSY | sample_4 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY-TROSY | sample_5 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_5 | isotropic | sample_conditions_1 |
| 2D 1H-15N TROSY-HSQC | sample_6 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
XEASY, Bartels et al. - data analysis
CcpNmr Analysis vVersion 2, Vranken et al - data analysis
TALOS+, Shen - data analysis
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement
NMR spectrometers:
- Bruker AVANCE 600 MHz
- Bruker AVANCE NEO 700 MHz
- Bruker AVANCE 800 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts