5JGF: MApe1

Crystal structure of mApe1. Determined by X-ray diffraction at 1.83 Å resolution. Released 29 Jun 2016.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 16,586
Mol. weight: 209.24 kDa
Ligands: ZN
Released: 29 Jun 2016

Explore 5JGF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JGF contains 94 α-helices and 112 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: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	48-62	15
α-helix	66-79	14
α-helix	82	1
β-strand	83-84	2	1
β-strand	100-106	7	1
β-strand	110-116	7	1
α-helix	122-124	3
β-strand	127-132	6	1
β-strand	137-140	4	2
β-strand	149	1	3
β-strand	152	1	3
β-strand	153-154	2	4
β-strand	157-160	4	2
α-helix	166-168	3
β-strand	173-181	9	2
β-strand	190-195	6	2
β-strand	202	1	2
β-strand	203	1	4
α-helix	205-208	4
α-helix	209-211	3
α-helix	213-215	3
β-strand	228-230	3	4
α-helix	241-243	3
α-helix	246-248	3
β-strand	252	1	5
β-strand	255	1	5
α-helix	257-267	11
α-helix	271-273	3
β-strand	274-283	10	2
α-helix	285-287	3
β-strand	288-290	3	6
β-strand	296-299	4	6
α-helix	302-319	18
β-strand	330-336	7	1
α-helix	339-341	3
α-helix	349-351	3
α-helix	353-365	13
α-helix	372-377	6
β-strand	380-384	5	1
β-strand	387-388	2	7
α-helix	389-390	2
α-helix	395-397	3
β-strand	411-413	3	1
α-helix	424-437	14
β-strand	442-444	3	1
α-helix	457-464	8
β-strand	467-472	6	1
β-strand	474-475	2	7
β-strand	476	1	6
β-strand	483-486	4	6
α-helix	489-508	20

Chain B: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	48-62	15
α-helix	66-79	14
α-helix	82	1
β-strand	83-84	2	8
β-strand	100-106	7	8
β-strand	110-116	7	8
α-helix	122-124	3
β-strand	127-132	6	8
β-strand	137-140	4	9
β-strand	149	1	10
β-strand	152	1	10
β-strand	153-154	2	11
β-strand	157-160	4	9
α-helix	166-168	3
β-strand	173-182	10	9
β-strand	189-195	7	9
β-strand	202	1	9
β-strand	203	1	11
α-helix	205-208	4
α-helix	209-211	3
α-helix	213-215	3
β-strand	228-230	3	11
α-helix	241-243	3
α-helix	246-248	3
β-strand	252	1	12
β-strand	255	1	12
α-helix	257-267	11
α-helix	271-273	3
β-strand	274-283	10	9
α-helix	285-287	3
β-strand	288-290	3	13
β-strand	296-299	4	13
α-helix	302-320	19
α-helix	324-326	3
β-strand	330-336	7	8
α-helix	339-341	3
α-helix	349-351	3
α-helix	353-365	13
α-helix	372-377	6
β-strand	380-384	5	8
β-strand	387-388	2	14
α-helix	389-390	2
α-helix	395-397	3
β-strand	411-413	3	8
α-helix	424-437	14
β-strand	442-444	3	8
α-helix	457-464	8
β-strand	467-472	6	8
β-strand	474-475	2	14
β-strand	476	1	13
β-strand	483-486	4	13
α-helix	489-509	21

Chain C: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	48-62	15
α-helix	66-79	14
α-helix	82	1
β-strand	83-84	2	15
β-strand	99-106	8	15
β-strand	110-117	8	15
α-helix	122-124	3
β-strand	127-132	6	15
β-strand	137-140	4	16
β-strand	149	1	17
β-strand	152	1	17
β-strand	153-154	2	18
β-strand	157-160	4	16
α-helix	166-168	3
β-strand	173-181	9	16
β-strand	190-195	6	16
β-strand	202	1	16
β-strand	203	1	18
α-helix	205-208	4
α-helix	209-211	3
α-helix	213-215	3
β-strand	228-230	3	18
α-helix	241-243	3
α-helix	246-248	3
β-strand	252	1	19
β-strand	255	1	19
α-helix	257-267	11
α-helix	271-273	3
β-strand	274-283	10	16
α-helix	285-287	3
β-strand	288-290	3	20
β-strand	296-299	4	20
α-helix	302-319	18
α-helix	324-326	3
β-strand	330-336	7	15
α-helix	339-341	3
α-helix	349-351	3
α-helix	353-365	13
α-helix	372-377	6
β-strand	380-384	5	15
β-strand	387-388	2	21
α-helix	389-390	2
α-helix	395-397	3
β-strand	410-413	4	15
α-helix	424-437	14
β-strand	441-444	4	15
α-helix	457-464	8
β-strand	467-472	6	15
β-strand	474-475	2	21
β-strand	476	1	20
β-strand	483-486	4	20
α-helix	489-509	21

Chain D: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	48-62	15
α-helix	66-79	14
α-helix	82	1
β-strand	83-84	2	22
β-strand	99-106	8	22
β-strand	110-117	8	22
α-helix	122-124	3
β-strand	127-132	6	22
β-strand	137-140	4	23
β-strand	149	1	24
β-strand	152	1	24
β-strand	153-154	2	25
β-strand	157-160	4	23
α-helix	166-168	3
β-strand	173-181	9	23
β-strand	190-195	6	23
β-strand	202	1	23
β-strand	203	1	25
α-helix	205-208	4
α-helix	209-211	3
α-helix	213-215	3
β-strand	228-230	3	25
α-helix	240-243	4
α-helix	246-248	3
β-strand	252	1	26
β-strand	255	1	26
α-helix	257-267	11
α-helix	271-273	3
β-strand	274-283	10	23
α-helix	285-287	3
β-strand	288-290	3	27
β-strand	296-299	4	27
α-helix	302-319	18
β-strand	330-336	7	22
α-helix	339-341	3
α-helix	349-351	3
α-helix	353-365	13
α-helix	372-377	6
β-strand	380-384	5	22
β-strand	387-388	2	28
α-helix	389-390	2
α-helix	395-397	3
β-strand	410-413	4	22
α-helix	424-437	14
β-strand	441-444	4	22
α-helix	457-464	8
β-strand	467-472	6	22
β-strand	474-475	2	28
β-strand	476	1	27
β-strand	483-486	4	27
α-helix	489-509	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar aminopeptidase 1	A, B, C, D	protein	473	Saccharomyces cerevisiae	P14904 (AlphaFold model)

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

>5JGF_1 Vacuolar aminopeptidase 1 (chains A, B, C, D)
GPHMEHNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGK
FYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYG
GTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDK
EDQTIPVIGFPTPDEEGNEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDL
FDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEI
GSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKN
HFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLA
SQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFGEL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates. Yamasaki, A., Watanabe, Y., Adachi, W. et al. Cell Rep (2016) 16:19-27. DOI 10.1016/j.celrep.2016.05.066 · PubMed

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

5JGE 1.91 Å, Crystal structure of Atg19 coiled-coil complexed with Ape1 propeptide
5JH9 2.1 Å, Crystal structure of prApe1
4R8F 2.5 Å, Crystal structure of yeast aminopeptidase 1 (Ape1)
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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