BMRB Entry 30553
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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/BMR30553
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Title: Structure of the transmembrane domain of the Death Receptor 5 - Dimer of Trimer PubMed: 30827683
Deposition date: 2018-12-24 Original release date: 2019-02-22
Authors: Chou, J.; Pan, L.; Fu, Q.; Zhao, L.; Chen, W.; Piai, A.; Fu, T.; Wu, H.
Citation: Pan, Liqiang; Fu, Tian-Min; Zhao, Wenbin; Zhao, Linlin; Chen, Wen; Qiu, Chixiao; Liu, Wenhui; Liu, Zhijun; Piai, Alessandro; Fu, Qingshan; Chen, Shuqing; Wu, Hao; Chou, James. "Higher-Order Clustering of the Transmembrane Anchor of DR5 Drives Signaling." Cell 176, 1477-1489.e14 (2019).
Assembly members:
entity_1, polymer, 36 residues, 3725.699 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 BL21(DE3)
Entity Sequences (FASTA):
entity_1: MPGSLSGIIIGVTVAAVVLI
VAVFVCKSLLWKKVLP
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 66 |
| 15N chemical shifts | 32 |
| 1H chemical shifts | 32 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1, 1 | 1 |
| 2 | entity_1, 2 | 1 |
| 3 | entity_1, 3 | 1 |
| 4 | entity_1, 4 | 1 |
| 5 | entity_1, 5 | 1 |
| 6 | entity_1, 6 | 1 |
Entities:
Entity 1, entity_1, 1 36 residues - 3725.699 Da.
| 1 | MET | PRO | GLY | SER | LEU | SER | GLY | ILE | ILE | ILE | ||||
| 2 | GLY | VAL | THR | VAL | ALA | ALA | VAL | VAL | LEU | ILE | ||||
| 3 | VAL | ALA | VAL | PHE | VAL | CYS | LYS | SER | LEU | LEU | ||||
| 4 | TRP | LYS | LYS | VAL | LEU | PRO |
Samples:
sample_1: Transmembrane Domain of Death Receptor 5, [U-13C; U-15N; 85%-2H], 0.8 ± 0.1 mM; DMPC 50 ± 3 mM; DHPC 100 ± 3 mM; sodium phosphate 20 ± 2 mM
sample_2: Transmembrane Domain of Death Receptor 5, [U-13C; U-15N], 0.8 ± 0.1 mM; DMPC, [acyl chain U-2H], 50 ± 3 mM; DHPC, [acyl chain U-2H], 100 ± 3 mM; sodium phosphate 20 ± 2 mM
sample_3: Transmembrane Domain of Death Receptor 5, [U-15N; U-2H; 15%-13C], 0.4 ± 0.1 mM; DMPC, [acyl chain U-2H], 50 ± 3 mM; DHPC, [acyl chain U-2H], 100 ± 3 mM; sodium phosphate 20 ± 2 mM
sample_conditions_1: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 303 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| TROSY-HSQC | sample_1 | isotropic | sample_conditions_1 |
| TROSY-HNCA | sample_1 | isotropic | sample_conditions_1 |
| TROSY-HNCOCA | sample_1 | isotropic | sample_conditions_1 |
| TROSY-HNCACO | sample_1 | isotropic | sample_conditions_1 |
| TROSY-HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D 15N NOE-TROSY-HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D 15N NOE-TROSY-HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D 13C NOE-HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_3 | isotropic | sample_conditions_1 |
| 3D 15N NOE-TROSY-HSQC | sample_3 | isotropic | sample_conditions_1 |
Software:
X-PLOR NIH v3.851, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CcpNMR, CCPN - chemical shift assignment
XEASY, Bartels et al. - chemical shift assignment
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 750 MHz
- Bruker Avance 900 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts