8W8M: Helical filament of MyD88 TIR

Cryo-EM structure of helical filament of MyD88 TIR. Determined by electron microscopy at 3.28 Å resolution. Released 4 Sept 2024.

Method: Electron microscopy
Resolution: 3.28 Å
Organism: Homo sapiens
Chains: 102
Atoms: 113,934
Mol. weight: 1717.86 kDa
Released: 4 Sept 2024

Explore 8W8M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W8M contains 945 α-helices and 710 β-strands across 102 chains. 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 1A: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	163-166	4	201
α-helix	173-183	11
β-strand	191-192	2	201
α-helix	194-197	4
β-strand	203	1	202
α-helix	204-206	3
α-helix	207-211	5
α-helix	212-214	3
β-strand	218-223	6	201
α-helix	226-228	3
α-helix	231-243	13
β-strand	253-256	4	201
α-helix	263-265	3
β-strand	271	1	181
β-strand	274-275	2	201
α-helix	285-294	10

Chain 1B: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	163-166	4	97
α-helix	173-182	10
β-strand	191-192	2	97
α-helix	194-197	4
β-strand	203	1	52
α-helix	204-210	7
α-helix	211-215	5
β-strand	219-223	5	97
α-helix	226-228	3
α-helix	232-243	12
β-strand	253-256	4	97
α-helix	263-265	3
α-helix	266-268	3
β-strand	271	1	202
β-strand	274-275	2	97
α-helix	279-284	6
α-helix	285-293	9

Chain 1C: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	163-166	4	50
α-helix	173-178	6
α-helix	179-183	5
β-strand	191-192	2	50
α-helix	194-197	4
β-strand	203	1	51
α-helix	204-206	3
α-helix	207-211	5
α-helix	212-214	3
β-strand	219-223	5	50
α-helix	226-228	3
α-helix	231-243	13
β-strand	253-256	4	50
α-helix	263-265	3
β-strand	271	1	52
β-strand	274-275	2	50
α-helix	285-294	10

Chain 1D: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	163-166	4	72
α-helix	173-182	10
β-strand	191-192	2	72
α-helix	194-197	4
β-strand	203	1	73
α-helix	204-206	3
α-helix	207-211	5
α-helix	212-214	3
β-strand	219-223	5	72
α-helix	226-229	4
α-helix	231-243	13
β-strand	253-256	4	72
α-helix	263-265	3
α-helix	266-268	3
β-strand	271	1	51
β-strand	274-275	2	72
α-helix	282-284	3
α-helix	285-294	10

Chain 1E: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	164-166	3	129
α-helix	173-183	11
β-strand	192	1	129
α-helix	194-197	4
β-strand	203	1	130
α-helix	204-206	3
α-helix	207-211	5
α-helix	212-214	3
β-strand	219-223	5	129
α-helix	226-228	3
α-helix	231-243	13
β-strand	253-256	4	129
α-helix	263-265	3
β-strand	271	1	73
β-strand	274-275	2	129
α-helix	285-293	9

Chain 1F: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	163-166	4	150
α-helix	173-183	11
β-strand	191-192	2	150
β-strand	203	1	84
α-helix	206	1
α-helix	207-211	5
α-helix	212-214	3
β-strand	219-223	5	150
α-helix	226-228	3
α-helix	232-243	12
β-strand	253-256	4	150
α-helix	263-265	3
α-helix	266-268	3
β-strand	271	1	130
β-strand	274-275	2	150
α-helix	285-294	10

Chain 2A: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	163-166	4	8
α-helix	173-182	10
β-strand	191-192	2	8
α-helix	194-197	4
β-strand	203	1	189
α-helix	204-214	11
β-strand	219-223	5	8
α-helix	226-228	3
α-helix	231-243	13
β-strand	253-256	4	8
α-helix	263-265	3
α-helix	266-268	3
β-strand	271	1	9
β-strand	274-275	2	8
α-helix	285-294	10

Chains 2B and S2: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	163-166	4	33
α-helix	173-182	10
β-strand	191-192	2	33
α-helix	194-197	4
β-strand	203	1	9
α-helix	204-214	11
β-strand	219-223	5	33
α-helix	226-228	3
α-helix	231-243	13
β-strand	253-256	4	33
α-helix	263-265	3
β-strand	271	1	34
β-strand	274-275	2	33
α-helix	285-293	9

87 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myeloid differentiation primary response protein MyD88	1A, 1B, 1C, 1D, 1E, 1F, 2A, 2B, 2C, 2D, 2E, 2F, 3A, 3B, 3C, 3D, 3E, 3F, A1, A2, A3, B1, B2, B3, C1, C2, C3, D1, D2, D3, E1, E2, E3, F1, F2, F3, G1, G2, G3, H1, H2, H3, I1, I2, I3, J1, J2, J3, K1, K2, K3, L1, L2, L3, M1, M2, M3, N1, N2, N3, O1, O2, O3, P1, P2, P3, Q1, Q2, Q3, R1, R2, R3, S1, S2, S3, T1, T2, T3, U1, U2, U3, V1, V2, V3, W1, W2, W3, X1, X2, X3, Y1, Y2, Y3, YD, YE, YF, Z1, Z2, Z3, ZD, ZE, ZF	protein	144	Homo sapiens	Q99836 (AlphaFold model)

Sequence of entity 1 (1A, 1B, 1C, 1D, 1E, 1F, 2A, 2B, 2C, 2D, 2E, 2F, 3A, 3B, 3C, 3D, 3E, 3F, A1, A2, A3, B1, B2, B3, C1, C2, C3, D1, D2, D3, E1, E2, E3, F1, F2, F3, G1, G2, G3, H1, H2, H3, I1, I2, I3, J1, J2, J3, K1, K2, K3, L1, L2, L3, M1, M2, M3, N1, N2, N3, O1, O2, O3, P1, P2, P3, Q1, Q2, Q3, R1, R2, R3, S1, S2, S3, T1, T2, T3, U1, U2, U3, V1, V2, V3, W1, W2, W3, X1, X2, X3, Y1, Y2, Y3, YD, YE, YF, Z1, Z2, Z3, ZD, ZE, ZF), FASTA

>8W8M_1 Myeloid differentiation primary response protein MyD88 (chains 1A, 1B, 1C, 1D, 1E, 1F, 2A, 2B, 2C, 2D, 2E, 2F, 3A, 3B, 3C, 3D, 3E, 3F, A1, A2, A3, B1, B2, B3, C1, C2, C3, D1, D2, D3, E1, E2, E3, F1, F2, F3, G1, G2, G3, H1, H2, H3, I1, I2, I3, J1, J2, J3, K1, K2, K3, L1, L2, L3, M1, M2, M3, N1, N2, N3, O1, O2, O3, P1, P2, P3, Q1, Q2, Q3, R1, R2, R3, S1, S2, S3, T1, T2, T3, U1, U2, U3, V1, V2, V3, W1, W2, W3, X1, X2, X3, Y1, Y2, Y3, YD, YE, YF, Z1, Z2, Z3, ZD, ZE, ZF)
PLGHMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELI
EKRCRRMVVVVSDDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFPSILRFIT
VCDYTNPCTKSWFWTRLAKALSLP

Primary citation

Structural Mechanism of Receptor-Triggered MyD88 Oligomeric Assembly in Innate Immune Signaling. Kasai, K., Imamura, K., Uno, M. et al. Nat Commun (2026). DOI 10.1038/s41467-026-71836-8 · 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
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
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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