6MB2: PYD filament of AIM2

Cryo-EM structure of the PYD filament of AIM2. Determined by electron microscopy at 5.0 Å resolution. Released 5 Sept 2018.

Method: Electron microscopy
Resolution: 5.0 Å
Organisms: Homo sapiens, Aequorea victoria
Chains: 30
Atoms: 37,650
Mol. weight: 551.46 kDa
Released: 5 Sept 2018

Explore 6MB2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MB2 contains 195 α-helices and 210 β-strands across 30 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.

Chains a, b, c, d, e, f, g, h, i, j, k, l, m, n and o: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	12-22	11	9
β-strand	25-36	12	9
β-strand	41-48	8	9
α-helix	57-60	4
α-helix	69-71	3
β-strand	73	1	9
α-helix	74-75	2
α-helix	76-81	6
α-helix	83-86	4
β-strand	92-100	9	9
β-strand	105-115	11	9
β-strand	118-128	11	9
β-strand	141	1	10
β-strand	148-155	8	9
β-strand	160-170	11	9
β-strand	171	1	10
β-strand	176-187	12	9
α-helix	195-197	3
β-strand	199-208	10	9
β-strand	217-227	11	9

Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N and O: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	1-7	7
α-helix	8-14	7
α-helix	20-27	8
α-helix	45-55	11
α-helix	60-71	12
α-helix	76-91	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interferon-inducible protein AIM2	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	protein	94	Homo sapiens	O14862 (AlphaFold model)
Green fluorescent protein	a, b, c, d, e, f, g, h, i, j, k, l, m, n, o	protein	226	Aequorea victoria	P42212 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O), FASTA

>6MB2_1 Interferon-inducible protein AIM2 (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O)
AMESKYKEILLLTGLDNITDEELDRFKGFLSDEFNIATGKLHTANRIQVATLMIQNAGAV
SAVMKTIRIFQKLNYMLLAKRLQEEKEKVDKQYK

Sequence of entity 2 (a, b, c, d, e, f, g, h, i, j, k, l, m, n, o), FASTA

>6MB2_2 Green fluorescent protein (chains a, b, c, d, e, f, g, h, i, j, k, l, m, n, o)
SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLV
TTFXVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRI
ELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQ
QNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGI

Primary citation

Plasticity in PYD assembly revealed by cryo-EM structure of the PYD filament of AIM2. Lu, A., Li, Y., Yin, Q. et al. Cell Discov (2015) 1. DOI 10.1038/celldisc.2015.13 · PubMed

Other PDB entries of the same protein (UniProt O14862 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4O7Q 1.82 Å, Crystal Structure of the F27G AIM2 Pyrin Domain Mutant and Similarities of its…
3VD8 2.07 Å, Crystal structure of human AIM2 PYD domain with MBP fusion
3RN5 2.5 Å, Structural basis of cytosolic DNA recognition by innate immune receptors
3RN2 2.55 Å, Structural Basis of Cytosolic DNA Recognition by Innate Immune Receptors
7K3R 3.2 Å, Cryo-EM structure of AIM2-PYD filament

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