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
MolProbity Validation Chart

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Title:
Solution structure of the TIR domain of human MyD88
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:

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).
PubMed: 19506249

Assembly members:

Assembly members:
MyD88 TIR domain, polymer, 149 residues, 17387.422 Da.

Natural source:

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-5X-3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MyD88 TIR domain: TTLDDPLGHMPERFDAFICY CPSDIQFVQEMIRQLEQTNY RLKLCVSDRDVLPGTCVWSI ASELIEKRCRRMVVVVSDDY LQSKECDFQTKFALSLSPGA HQKRLIPIKYKAMKKEFPSI LRFITVCDYTNPCTKSWFWT RLAKALSLP

Data sets:
Data typeCount
13C chemical shifts454
15N chemical shifts134
1H chemical shifts850

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1MyD88 TIR domain1

Entities:

Entity 1, MyD88 TIR domain 149 residues - 17387.422 Da.

1   THRTHRLEUASPASPPROLEUGLYHISMET
2   PROGLUARGPHEASPALAPHEILECYSTYR
3   CYSPROSERASPILEGLNPHEVALGLNGLU
4   METILEARGGLNLEUGLUGLNTHRASNTYR
5   ARGLEULYSLEUCYSVALSERASPARGASP
6   VALLEUPROGLYTHRCYSVALTRPSERILE
7   ALASERGLULEUILEGLULYSARGCYSARG
8   ARGMETVALVALVALVALSERASPASPTYR
9   LEUGLNSERLYSGLUCYSASPPHEGLNTHR
10   LYSPHEALALEUSERLEUSERPROGLYALA
11   HISGLNLYSARGLEUILEPROILELYSTYR
12   LYSALAMETLYSLYSGLUPHEPROSERILE
13   LEUARGPHEILETHRVALCYSASPTYRTHR
14   ASNPROCYSTHRLYSSERTRPPHETRPTHR
15   ARGLEUALALYSALALEUSERLEUPRO

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_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
AlphaFold B3Y678 B3Y679 B3Y680 B3Y681 B3Y682

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks