7BER: PDB entry 7BER

SFX structure of the MyD88 TIR domain higher-order assembly (solved, rebuilt and refined using an identical protocol to the MicroED structure of the MyD88 TIR domain higher-order assembly). Determined by X-ray diffraction at 2.3 Å resolution. Released 10 Mar 2021.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,133
Mol. weight: 17.83 kDa
Released: 10 Mar 2021

Explore 7BER in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BER contains 12 α-helices and 5 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: 12 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	161-166	6	1
α-helix	169-171	3
α-helix	172-182	11
β-strand	191-192	2	1
α-helix	194-197	4
α-helix	199	1
α-helix	204-210	7
α-helix	211-215	5
β-strand	216-223	8	1
α-helix	225-228	4
α-helix	231-243	13
β-strand	252-256	5	1
α-helix	263-265	3
α-helix	266-268	3
β-strand	274-275	2	1
α-helix	282-284	3
α-helix	285-292	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myeloid differentiation primary response protein MyD88	A	protein	151	Homo sapiens	Q99836 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7BER_1 Myeloid differentiation primary response protein MyD88 (chains A)
MGHMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIE
KRCRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFPSILRFITV
CDYTNPCTKSWFWTRLAKALSLPLEHHHHHH

Primary citation

MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Clabbers, M.T.B., Holmes, S., Muusse, T.W. et al. Nat Commun (2021) 12:2578-2578. DOI 10.1038/s41467-021-22590-6 · 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
4DOM 1.8 Å, Crystal Structure of the TIR-domain of Human Myeloid Differentiation Primary Response…
9HGH 1.9 Å, MyD88 peptide_1 bound to SPOP MATH domain
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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