9C9I: TSC1:WIPI3 complex

Structure of the TSC1:WIPI3 complex. Determined by X-ray diffraction at 3.18 Å resolution. Released 4 Dec 2024.

Method: X-ray diffraction
Resolution: 3.18 Å
Organism: Homo sapiens
Chains: 9
Atoms: 10,118
Mol. weight: 158.34 kDa
Released: 4 Dec 2024

Explore 9C9I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C9I contains 16 α-helices and 113 β-strands across 9 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 A: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
β-strand	24-29	6	1
β-strand	33-37	5	1
β-strand	42-47	6	1
β-strand	56-59	4	2
β-strand	65-69	5	2
β-strand	75-80	6	2
β-strand	85-91	7	2
β-strand	96-101	6	3
β-strand	105-110	6	3
β-strand	113-118	6	3
β-strand	127-130	4	3
β-strand	140-141	2	4
β-strand	149-153	5	4
β-strand	160-164	5	4
α-helix	171-172	2
β-strand	173-175	3	4
β-strand	182-187	6	5
β-strand	193-198	6	5
β-strand	203-208	6	5
β-strand	214-219	6	5
β-strand	229-232	4	6
β-strand	238-243	6	6
α-helix	244-246	3
β-strand	247-252	6	6
β-strand	263-266	4	6
β-strand	273-277	5	7
β-strand	283-288	6	7
β-strand	292-298	7	7
β-strand	304-311	8	7
α-helix	312-314	3

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	660-665	6
α-helix	669-672	4

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	8
β-strand	24-29	6	8
β-strand	33-37	5	8
β-strand	42-47	6	8
β-strand	56-59	4	9
β-strand	65-69	5	9
β-strand	75-80	6	9
β-strand	85-91	7	9
β-strand	96-101	6	10
β-strand	105-110	6	10
β-strand	113-118	6	10
β-strand	125-130	6	10
β-strand	140-141	2	11
β-strand	149-153	5	11
β-strand	160-164	5	11
β-strand	173-175	3	11
α-helix	181	1
β-strand	182-187	6	12
β-strand	193-198	6	12
β-strand	203-208	6	12
β-strand	214-219	6	12
α-helix	220-221	2
β-strand	230-232	3	13
β-strand	238-242	5	13
β-strand	247-252	6	13
β-strand	263-266	4	13
β-strand	273-277	5	14
β-strand	283-288	6	14
β-strand	293-298	6	14
β-strand	304-310	7	14
α-helix	312-314	3

Chains D and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	669-672	4

Chain E: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	15-18	4	15
β-strand	24-28	5	15
β-strand	32-37	6	15
β-strand	42-48	7	15
β-strand	56-59	4	16
β-strand	65-69	5	16
β-strand	75-80	6	16
β-strand	85-91	7	16
β-strand	96-102	7	17
β-strand	105-110	6	17
β-strand	113-118	6	17
β-strand	127-130	4	17
β-strand	140-141	2	18
β-strand	149-153	5	18
β-strand	159-164	6	18
α-helix	171-172	2
β-strand	173-176	4	18
β-strand	182-187	6	19
β-strand	193-198	6	19
β-strand	203-208	6	19
β-strand	214-219	6	19
β-strand	230-232	3	20
β-strand	238-242	5	20
β-strand	247-252	6	20
β-strand	263-266	4	20
β-strand	273-277	5	7
β-strand	283-288	6	7
β-strand	292-298	7	7
β-strand	304-311	8	7
α-helix	312-314	3

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	660-666	7
α-helix	669-672	4

Chain G: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	21
β-strand	24-29	6	21
β-strand	33-37	5	21
β-strand	42-47	6	21
β-strand	57-59	3	22
β-strand	65-69	5	22
β-strand	75-80	6	22
β-strand	85-91	7	22
β-strand	98-101	4	23
β-strand	105-109	5	23
β-strand	113-118	6	23
β-strand	125-130	6	23
β-strand	140-141	2	24
β-strand	149-153	5	24
β-strand	160-164	5	24
β-strand	173-175	3	24
α-helix	181	1
β-strand	182-187	6	25
β-strand	193-198	6	25
β-strand	203-208	6	25
β-strand	214-219	6	25
β-strand	229-232	4	26
β-strand	238-242	5	26
α-helix	244-246	3
β-strand	247-252	6	26
β-strand	263-266	4	26
β-strand	273-277	5	27
β-strand	283-288	6	27
β-strand	292-298	7	27
β-strand	304-311	8	27

Chain X: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	11-14	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
WD repeat domain phosphoinositide-interacting protein 3	A, C, E, G	protein	316	Homo sapiens	Q5MNZ6 (AlphaFold model)
Hamartin	B, D, F, H, X	protein	34	Homo sapiens	Q92574 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>9C9I_1 WD repeat domain phosphoinositide-interacting protein 3 (chains A, C, E, G)
MHHHHHHGLLYAGFNQDHGCFACGMENGFRVYNTDPLKEKEKQEFLEGGVGHVEMLFRCN
YLALVGGGKKKVMIWDDLKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVFTFTHNPH
QLHVFETCYNPKGLCVLCPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSC
IALNLQGTRIATASEKGTLIRIFDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSD
HGTVHIFAAEDPKSKWSFSKFQVPSGSPCICAFGTEPNAVIAICADGSYYKFLFNPKGEC
IRDVYAQFLEMTDDKL

Sequence of entity 2 (B, D, F, H, X), FASTA

>9C9I_2 Hamartin (chains B, D, F, H, X)
XXXXXXXXXXXAHSKELNKLPLPSKSVDWTHFGG

Primary citation

Structure of the human TSC:WIPI3 lysosomal recruitment complex. Bayly-Jones, C., Lupton, C.J., D'Andrea, L. et al. Sci Adv (2024) 10:eadr5807-eadr5807. DOI 10.1126/sciadv.adr5807 · PubMed

Other PDB entries of the same protein (UniProt Q5MNZ6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6IYY 1.8 Å, Crystal structure of human WIPI3,loop deletion mutant
6KLR 2.21 Å, Crystal structure of human WIPI3 in complex with the WIR-peptide from ATG2A
8ZQG 2.77 Å, Crystal structure of WIPI3 in complex with ATG16L1
9CE3 2.9 Å, Structure of the TSC:WIPI3 lysosomal recruitment complex

Browse structure collections

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