7XFR: WIPI2b

Crystal structure of WIPI2b in complex with the second site of ATG16L1. Determined by X-ray diffraction at 1.76 Å resolution. Released 8 Mar 2023.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,431
Mol. weight: 86.25 kDa
Released: 8 Mar 2023

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

Secondary structure: helices and β-sheets

7XFR contains 8 α-helices and 58 β-strands across 4 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, 29 β-strands

Element	Residues	Length	Sheet
β-strand	15-20	6	1
β-strand	26-31	6	1
β-strand	34-39	6	1
β-strand	48-52	5	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	80-85	6	2
β-strand	91-96	6	2
β-strand	103-106	4	3
β-strand	110-114	5	3
β-strand	118-123	6	3
β-strand	129-134	6	3
α-helix	136	1
α-helix	138	1
β-strand	145-146	2	4
β-strand	154-158	5	4
β-strand	164-170	7	4
β-strand	175-183	9	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	208-213	6	5
β-strand	219-224	6	5
β-strand	233-238	6	6
β-strand	244-249	6	6
β-strand	253-258	6	6
β-strand	303-306	4	6
β-strand	314-321	8	7
β-strand	324-331	8	7
β-strand	335-340	6	7
β-strand	347-348	2	6
α-helix	349-350	2
β-strand	351-356	6	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	127-186	60

Chain C: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	15-20	6	8
β-strand	26-31	6	8
β-strand	34-39	6	8
β-strand	48-52	5	8
β-strand	58-63	6	9
β-strand	69-74	6	9
β-strand	77-85	9	9
β-strand	90-96	7	9
β-strand	103-106	4	10
β-strand	110-114	5	10
β-strand	118-123	6	10
β-strand	129-134	6	10
α-helix	136-138	3
β-strand	145-146	2	11
β-strand	154-158	5	11
β-strand	164-170	7	11
β-strand	175-183	9	11
α-helix	186	1
β-strand	187-192	6	12
β-strand	198-203	6	12
β-strand	208-213	6	12
β-strand	219-224	6	12
β-strand	233-238	6	13
β-strand	244-249	6	13
β-strand	253-258	6	13
β-strand	303-306	4	13
β-strand	314-321	8	14
β-strand	324-331	8	14
β-strand	335-340	6	14
β-strand	347-348	2	13
α-helix	349-350	2
β-strand	351-356	6	14

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	127-185	59

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2	A, C	protein	321	Homo sapiens	Q9Y4P8 (AlphaFold model)
Autophagy-related protein 16-1	B, D	protein	69	Homo sapiens	Q676U5 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7XFR_1 Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2 (chains A, C)
GPGSGQLLFANFNQDNTSLAVGSKSGYKFFSLSSVDKLEQIYECTDTEDVCIVERLFSSS
LVAIVSLKAPRKLKVCHFKKGTEICNYSYSNTILAVKLNRQRLIVCLEESLYIHNIRDMK
VLHTIRETPPNPAGLCALSINNDNCYLAYPGSATIGEVQVFDTINLRAANMIPAHDSPLA
ALAFDASGTKLATASEKGTVIRVFSIPEGQKLFEFRRGVKRCVSICSLAFSMDGMFLSAS
SNTETVHIFKLETVKEQGRAFATVRLPFCGHKNICSLATIQKIPRLLVGAADGYLYMYNL
DPQEGGECALMKQHRLDGSLE

Sequence of entity 2 (B, D), FASTA

>7XFR_2 Autophagy-related protein 16-1 (chains B, D)
GPGSMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGK
LRKTTEENQ

Primary citation

ATG16L1 adopts a dual-binding site mode to interact with WIPI2b in autophagy. Gong, X., Wang, Y., Tang, Y. et al. Sci Adv (2023) 9:eadf0824-eadf0824. DOI 10.1126/sciadv.adf0824 · PubMed

Other PDB entries of the same protein (UniProt Q9Y4P8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7F69 1.5 Å, Crystal structure of WIPI2b in complex with ATG16L1
7MU2 1.85 Å, Crystal Structure of WIPI2 in complex with W2IR of ATG16L1

Browse structure collections

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