5JH9: PrApe1

Crystal structure of prApe1. Determined by X-ray diffraction at 2.1 Å resolution. Released 29 Jun 2016.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 15,486
Mol. weight: 230.78 kDa
Ligands: ZN, CAC
Released: 29 Jun 2016

Explore 5JH9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JH9 contains 97 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: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	34-43	10
α-helix	49-62	14
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	137-145	9	2
β-strand	149	1	3
β-strand	152	1	3
β-strand	153-154	2	4
β-strand	155-160	6	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	244-247	4
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	302-320	19
β-strand	330-336	7	1
α-helix	339-341	3
α-helix	349-351	3
α-helix	353-366	14
α-helix	372-377	6
β-strand	380-384	5	1
β-strand	387-388	2	7
α-helix	395-397	3
β-strand	410-413	4	1
α-helix	424-437	14
β-strand	441-444	4	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
α-helix	509-511	3

Chain B: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	32-42	11
α-helix	50-62	13
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	137-145	9	9
β-strand	149	1	10
β-strand	152	1	10
β-strand	153-154	2	11
β-strand	155-160	6	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
β-strand	288-290	3	13
β-strand	296-299	4	13
α-helix	302-320	19
β-strand	330-336	7	8
α-helix	349-351	3
α-helix	353-366	14
α-helix	372-377	6
β-strand	380-384	5	8
β-strand	387-388	2	14
α-helix	395-397	3
α-helix	399	1
β-strand	410-413	4	8
α-helix	424-437	14
β-strand	441-444	4	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	489-508	20
α-helix	509-511	3

Chain C: 25 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	36-43	8
α-helix	50-62	13
α-helix	66-79	14
α-helix	82	1
β-strand	83-84	2	15
β-strand	100-106	7	15
β-strand	110-116	7	15
α-helix	122-124	3
β-strand	127-132	6	15
β-strand	137-140	4	16
α-helix	141	1
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	173-182	10	16
β-strand	189-195	7	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	244-247	4
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
β-strand	288-290	3	20
β-strand	296-299	4	20
α-helix	302-320	19
α-helix	324-326	3
β-strand	330-336	7	15
α-helix	339-341	3
α-helix	349-351	3
α-helix	353-366	14
α-helix	372-377	6
β-strand	380-384	5	15
β-strand	387-388	2	21
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	489-508	20
α-helix	509-511	3

Chain D: 25 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	36-42	7
α-helix	49-62	14
α-helix	66-79	14
α-helix	82	1
β-strand	83-84	2	22
α-helix	91-93	3
β-strand	100-106	7	22
β-strand	110-116	7	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	173-182	10	23
β-strand	189-195	7	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	353-366	14
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	516	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P14904 (AlphaFold model)

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

>5JH9_1 Vacuolar aminopeptidase 1 (chains A, B, C, D)
GPMEEQREILEQSKKTLQMLTVEPSKNNQIANEEKEKKENENSWCILEHNYEDIAQEFID
FIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGK
NWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGR
LLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQTIPVIGFPTPDEEG
NEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLF
APRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVV
ERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNG
HMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQTGARTIDLGIAQLSM
HSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFGEL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
CAC	Cacodylate ion	C2 H6 As O2	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:

5JGF 1.83 Å, Crystal structure of mApe1
5JGE 1.91 Å, Crystal structure of Atg19 coiled-coil complexed with Ape1 propeptide
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

About this viewer

MolViewer shows 5JH9 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.