4DOM: PDB entry 4DOM

Crystal Structure of the TIR-domain of Human Myeloid Differentiation Primary Response protein (MyD88). Determined by X-ray diffraction at 1.8 Å resolution. Released 10 Apr 2013.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,272
Mol. weight: 16.72 kDa
Released: 10 Apr 2013

Explore 4DOM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DOM contains 13 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	161-166	6	1
α-helix	169-171	3
α-helix	172-183	12
β-strand	191-193	3	1
α-helix	196-198	3
β-strand	205-206	2	1
α-helix	209-211	3
α-helix	212-215	4
β-strand	216-223	8	1
α-helix	225-228	4
α-helix	231-242	12
α-helix	244	1
α-helix	248-251	4
β-strand	252-256	5	1
α-helix	263-265	3
α-helix	266-268	3
β-strand	274-275	2	1
α-helix	279-281	3
α-helix	285-294	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myeloid differentiation primary response protein MyD88	A	protein	141	Homo sapiens	Q99836 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DOM_1 Myeloid differentiation primary response protein MyD88 (chains A)
DMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKR
CRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFPSILRFITVCD
YTNPCTKSWFWTRLAKALSLP

Primary citation

Molecular mechanisms for the subversion of MyD88 signaling by TcpC from virulent uropathogenic Escherichia coli. Snyder, G.A., Cirl, C., Jiang, J. et al. Proc Natl Acad Sci U S A (2013) 110:6985-6990. DOI 10.1073/pnas.1215770110 · PubMed

Other PDB entries of the same protein (UniProt Q99836 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4EO7 1.45 Å, Crystal structure of the TIR domain of human myeloid differentiation primary response…
9HFV 1.45 Å, MyD88 peptide_2 bound to SPOP MATH domain
9HGH 1.9 Å, MyD88 peptide_1 bound to SPOP MATH domain
7BER 2.3 Å, SFX structure of the MyD88 TIR domain higher-order assembly (solved, rebuilt and refined…
7L6W 2.3 Å, SFX structure of the MyD88 TIR domain higher-order assembly
8S78 2.85 Å, MicroED Structure of TLR2 TIR domain-induced MyD88 TIR domain higher-order assembly
7BEQ 3.0 Å, MicroED structure of the MyD88 TIR domain higher-order assembly
6I3N 3.1 Å, Helical MyD88 death domain filament
8W8M 3.28 Å, Cryo-EM structure of helical filament of MyD88 TIR
8YYM 3.3 Å, Cryo-EM structure of cylindrical fiber of MyD88 TIR
3MOP 3.4 Å, The ternary Death Domain complex of MyD88, IRAK4, and IRAK2
2JS7 Solution NMR structure of human myeloid differentiation primary response (MyD88).…

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