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BMRB: 11078

2Z5V

Solution structure of the TIR domain of human MyD88

Authors

Ohnishi, H., Tochio, H., Hiroaki, H., Kondo, N., Kato, Z., Shirakawa, M.

Assembly

Myeloid differentiation primary response protein MyD88

Entity

1. Myeloid differentiation primary response protein MyD88 (polymer, Thiol state: all free), 149 monomers, 17364.11 Da Detail

TTLDDPLGHM PERFDAFICY CPSDIQFVQE MIRQLEQTNY RLKLCVSDRD VLPGTCVWSI ASELIEKRCR RMVVVVSDDY LQSKECDFQT KFALSLSPGA HQKRLIPIKY KAMKKEFPSI LRFITVCDYT NPCTKSWFWT RLAKALSLP

Formula weight

17364.11 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.6 %, Completeness: 73.0 %, Completeness (bb): 77.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.0 % (1326 of 1817)	75.3 % (715 of 950)	66.2 % (473 of 715)	90.8 % (138 of 152)
Backbone	77.9 % (682 of 876)	89.4 % (261 of 292)	66.2 % (294 of 444)	90.7 % (127 of 140)
Sidechain	71.8 % (781 of 1087)	69.0 % (454 of 658)	75.8 % (316 of 417)	91.7 % (11 of 12)
Aromatic	28.7 % (47 of 164)	40.2 % (33 of 82)	13.9 % (11 of 79)	100.0 % (3 of 3)
Methyl	89.6 % (147 of 164)	85.4 % (70 of 82)	93.9 % (77 of 82)

1. MyD88 TIR domain

TTLDDPLGHM PERFDAFICY CPSDIQFVQE MIRQLEQTNY RLKLCVSDRD VLPGTCVWSI ASELIEKRCR RMVVVVSDDY LQSKECDFQT KFALSLSPGA HQKRLIPIKY KAMKKEFPSI LRFITVCDYT NPCTKSWFWT RLAKALSLP

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	MyD88 TIR domain	[U-100% 13C; U-100% 15N]	0.3 mM
2	potassium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	EDTA	natural abundance	0.1 mM
5	L-arginine	natural abundance	50 mM
6	L-glutamate	natural abundance	50 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
9	MyD88 TIR domain	[U-100% 13C; U-100% 15N]	0.2 mM
10	potassium phosphate	natural abundance	20 mM
11	DTT	natural abundance	10 mM
12	EDTA	natural abundance	0.1 mM
13	H2O	natural abundance	95 %
14	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2Z5V, Strand ID: A Detail

Release date

2010-03-11

Citation

Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling
Ohnishi, H., Tochio, H., Kato, Z., Orii, K.E., Li, A., Kimura, T., Hiroaki, H., Kondo, N., Shirakawa, M.
Proc. Natl. Acad. Sci. U. S. A. (2009), 106, 10260-10265, PubMed 19506249 , DOI 10.1073/pnas.0812956106 , Abstract

Related entities 1. Myeloid differentiation primary response protein MyD88, : 1 : 7 : 4 : 125 entities Detail

Interaction partners 1. Myeloid differentiation primary response protein MyD88, : 43 interactors Detail

More details for 43 interactors identified by 17 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC