BMRB Entry 11078
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11078
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Title: Solution structure of the TIR domain of human MyD88 PubMed: 19506249
Deposition date: 2009-09-11 Original release date: 2010-03-12
Authors: Ohnishi, H.; Tochio, H.; Hiroaki, H.; Kondo, N.; Kato, Z.; Shirakawa, M.
Citation: Ohnishi, Hidenori; Tochio, Hidehito; Kato, Zenichiro; Orii, Kenji; Li, Ailian; Kimura, Takeshi; Hiroaki, Hidekazu; Kondo, Naomi; Shirakawa, Masahiro. "Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling." Proc. Natl. Acad. Sci. U.S.A. 106, 10260-10265 (2009).
Assembly members:
MyD88 TIR domain, polymer, 149 residues, 17387.422 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):
MyD88 TIR domain: TTLDDPLGHMPERFDAFICY
CPSDIQFVQEMIRQLEQTNY
RLKLCVSDRDVLPGTCVWSI
ASELIEKRCRRMVVVVSDDY
LQSKECDFQTKFALSLSPGA
HQKRLIPIKYKAMKKEFPSI
LRFITVCDYTNPCTKSWFWT
RLAKALSLP
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 454 |
| 15N chemical shifts | 134 |
| 1H chemical shifts | 850 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | MyD88 TIR domain | 1 |
Entities:
Entity 1, MyD88 TIR domain 149 residues - 17387.422 Da.
| 1 | THR | THR | LEU | ASP | ASP | PRO | LEU | GLY | HIS | MET | ||||
| 2 | PRO | GLU | ARG | PHE | ASP | ALA | PHE | ILE | CYS | TYR | ||||
| 3 | CYS | PRO | SER | ASP | ILE | GLN | PHE | VAL | GLN | GLU | ||||
| 4 | MET | ILE | ARG | GLN | LEU | GLU | GLN | THR | ASN | TYR | ||||
| 5 | ARG | LEU | LYS | LEU | CYS | VAL | SER | ASP | ARG | ASP | ||||
| 6 | VAL | LEU | PRO | GLY | THR | CYS | VAL | TRP | SER | ILE | ||||
| 7 | ALA | SER | GLU | LEU | ILE | GLU | LYS | ARG | CYS | ARG | ||||
| 8 | ARG | MET | VAL | VAL | VAL | VAL | SER | ASP | ASP | TYR | ||||
| 9 | LEU | GLN | SER | LYS | GLU | CYS | ASP | PHE | GLN | THR | ||||
| 10 | LYS | PHE | ALA | LEU | SER | LEU | SER | PRO | GLY | ALA | ||||
| 11 | HIS | GLN | LYS | ARG | LEU | ILE | PRO | ILE | LYS | TYR | ||||
| 12 | LYS | ALA | MET | LYS | LYS | GLU | PHE | PRO | SER | ILE | ||||
| 13 | LEU | ARG | PHE | ILE | THR | VAL | CYS | ASP | TYR | THR | ||||
| 14 | ASN | PRO | CYS | THR | LYS | SER | TRP | PHE | TRP | THR | ||||
| 15 | ARG | LEU | ALA | LYS | ALA | LEU | SER | LEU | PRO |
Samples:
sample_1: MyD88 TIR domain, [U-100% 13C; U-100% 15N], 0.3 mM; potassium phosphate 20 mM; DTT 10 mM; EDTA 0.1 mM; L-arginine 50 mM; L-glutamate 50 mM; H2O 95%; D2O 5%
sample_2: MyD88 TIR domain, [U-100% 13C; U-100% 15N], 0.2 mM; potassium phosphate 20 mM; DTT 10 mM; EDTA 0.1 mM; H2O 95%; D2O 5%
sample_conditions_1: ionic strength: 120 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | 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 HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
Software:
CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker DRX 500 MHz
- Varian INOVA 900 MHz
Related Database Links:
| BMRB | 15356 |
| PDB | |
| DBJ | BAE89833 BAG55247 BAG55248 BAG55249 BAG55250 |
| GB | AAB49967 AAC50954 AAH13589 AAP36040 AAP36509 |
| REF | NP_001123935 NP_001124153 NP_001166039 NP_001266118 NP_001266529 |
| SP | B3Y678 B3Y679 B3Y680 B3Y681 B3Y682 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts