4R8F: Yeast aminopeptidase 1

Crystal structure of yeast aminopeptidase 1 (Ape1). Determined by X-ray diffraction at 2.5 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 4
Atoms: 13,635
Mol. weight: 207.55 kDa
Released: 12 Aug 2015

Explore 4R8F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4R8F contains 75 α-helices and 97 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: 21 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	9-18	10
α-helix	22-34	13
α-helix	38	1
β-strand	39-40	2	1
β-strand	56-62	7	1
β-strand	66-72	7	1
α-helix	78-80	3
β-strand	83-88	6	1
β-strand	93-105	13	2
β-strand	108-116	9	2
α-helix	122-124	3
β-strand	125	1	3
β-strand	129-137	9	2
β-strand	146-151	6	2
β-strand	158	1	2
β-strand	160	1	3
α-helix	161-163	3
β-strand	182-183	2	2
α-helix	197-199	3
α-helix	200-203	4
α-helix	213-223	11
α-helix	227-229	3
β-strand	230-239	10	2
β-strand	244-246	3	4
β-strand	252-255	4	4
α-helix	258-276	19
α-helix	280-282	3
β-strand	286-292	7	1
α-helix	305-307	3
α-helix	309-321	13
α-helix	328-333	6
β-strand	336-340	5	1
β-strand	344	1	5
α-helix	345-346	2
α-helix	351-353	3
α-helix	355	1
β-strand	366-370	5	1
α-helix	380-393	14
β-strand	397-401	5	1
α-helix	412-420	9
β-strand	423-428	6	1
β-strand	431	1	5
β-strand	432	1	4
β-strand	439-442	4	4
α-helix	445-465	21

Chain B: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
α-helix	22-35	14
α-helix	38	1
β-strand	39-40	2	6
β-strand	56-62	7	6
β-strand	66-72	7	6
α-helix	78-80	3
β-strand	83-88	6	6
β-strand	93-101	9	7
β-strand	110-116	7	7
β-strand	125	1	8
β-strand	129-138	10	7
β-strand	145-151	7	7
β-strand	158	1	7
β-strand	160	1	8
β-strand	182-183	2	7
α-helix	197-199	3
α-helix	200-203	4
α-helix	213-223	11
α-helix	227-229	3
β-strand	230-239	10	7
α-helix	241-243	3
β-strand	244-246	3	9
β-strand	252-255	4	9
α-helix	258-275	18
β-strand	286-292	7	6
α-helix	295-297	3
α-helix	305-307	3
α-helix	309-321	13
α-helix	328-333	6
β-strand	336-340	5	6
β-strand	344	1	10
α-helix	345-346	2
β-strand	367-370	4	6
α-helix	381-393	13
β-strand	398-401	4	6
α-helix	412-420	9
β-strand	423-428	6	6
β-strand	431	1	10
β-strand	432	1	9
β-strand	439-442	4	9
α-helix	445-465	21

Chain C: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
α-helix	22-35	14
α-helix	38	1
β-strand	39-40	2	11
β-strand	56-62	7	11
β-strand	66-72	7	11
α-helix	78-80	3
β-strand	83-88	6	11
β-strand	93-101	9	12
β-strand	105	1	13
β-strand	108	1	13
β-strand	110-116	7	12
α-helix	122-124	3
β-strand	129-137	9	12
β-strand	146-151	6	12
β-strand	158	1	12
β-strand	182-183	2	12
α-helix	197-199	3
α-helix	200-203	4
α-helix	213-223	11
α-helix	227-229	3
β-strand	230-239	10	12
α-helix	241-243	3
β-strand	244-246	3	14
β-strand	252-255	4	14
α-helix	258-276	19
β-strand	286-292	7	11
α-helix	305-307	3
α-helix	309-321	13
α-helix	325-326	2
α-helix	328-333	6
β-strand	336-340	5	11
β-strand	344	1	15
α-helix	351-353	3
β-strand	366-370	5	11
α-helix	380-393	14
β-strand	397-401	5	11
α-helix	412-420	9
β-strand	423-428	6	11
β-strand	431	1	15
β-strand	432	1	14
β-strand	439-442	4	14
α-helix	445-465	21

Chain D: 17 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
α-helix	22-35	14
β-strand	39-40	2	16
β-strand	56-62	7	16
β-strand	66-72	7	16
α-helix	78-80	3
β-strand	83-88	6	16
β-strand	93-101	9	17
β-strand	105	1	18
β-strand	108	1	18
β-strand	111-116	6	17
α-helix	122-124	3
β-strand	125	1	19
β-strand	129-138	10	17
β-strand	145-151	7	17
β-strand	158	1	17
β-strand	160	1	19
α-helix	197-199	3
α-helix	202-204	3
α-helix	213-223	11
β-strand	230-239	10	17
α-helix	241-243	3
β-strand	244-246	3	20
β-strand	252-255	4	20
α-helix	262-276	15
β-strand	286-292	7	16
α-helix	305-307	3
α-helix	309-321	13
α-helix	325-326	2
α-helix	328-333	6
β-strand	336-340	5	16
β-strand	343-344	2	21
β-strand	365-370	6	16
α-helix	375-378	4
α-helix	380-392	13
β-strand	396-401	6	16
α-helix	412-420	9
β-strand	423-428	6	16
β-strand	430-431	2	21
β-strand	432	1	20
β-strand	439-442	4	20
α-helix	445-465	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar aminopeptidase 1	A, B, C, D	protein	470	Saccharomyces cerevisiae S288c	P14904 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4R8F_1 Vacuolar aminopeptidase 1 (chains A, B, C, D)
MEHNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYT
IRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTL
NELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQ
TIPVIGFPTPDEEGNEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDV
QKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSL
TRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFP
VPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQT
GARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFGEL

Primary citation

Structure of yeast Ape1 and its role in autophagic vesicle formation. Su, M.Y., Peng, W.H., Ho, M.R. et al. Autophagy (2015) 11:1580-1593. DOI 10.1080/15548627.2015.1067363 · PubMed

Other PDB entries of the same protein (UniProt P14904 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JGF 1.83 Å, Crystal structure of mApe1
5JGE 1.91 Å, Crystal structure of Atg19 coiled-coil complexed with Ape1 propeptide
5JH9 2.1 Å, Crystal structure of prApe1
5JHC 3.4 Å, Crystal structure of the self-assembled propeptides from Ape1
5JM9 24.0 Å, Structure of S. cerevesiae mApe1 dodecamer

Browse structure collections

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