1HR6: Yeast Mitochondrial Processing Peptidase

Yeast Mitochondrial Processing Peptidase. Determined by X-ray diffraction at 2.5 Å resolution. Released 11 Jul 2001.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 28,061
Mol. weight: 406.45 kDa
Ligands: ZN
Released: 11 Jul 2001

Explore 1HR6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1HR6 contains 212 α-helices and 126 β-strands across 8 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.

Chains A and E: 29 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	20-23	4	1
β-strand	29-33	5	1
β-strand	40-46	7	1
α-helix	50-52	3
α-helix	60-66	7
β-strand	72	1	2
β-strand	75	1	2
α-helix	77-86	10
β-strand	91-95	5	1
β-strand	100-106	7	1
α-helix	108-110	3
α-helix	111-123	13
β-strand	125	1	2
α-helix	129-146	18
α-helix	150-162	13
α-helix	167-169	3
α-helix	174-175	2
α-helix	176-181	6
α-helix	184-194	11
α-helix	197-199	3
β-strand	200-205	6	1
α-helix	209-220	12
α-helix	228-230	3
α-helix	233-235	3
β-strand	240-244	5	3
α-helix	245-248	4
α-helix	254-255	2
β-strand	257-264	8	3
α-helix	273-283	11
β-strand	285-287	3	3
α-helix	301	1
α-helix	302-307	6
β-strand	313-322	10	3
β-strand	327-335	9	3
α-helix	337-339	3
α-helix	340-352	13
α-helix	361-363	3
α-helix	364-381	18
α-helix	385-399	15
α-helix	405-413	9
α-helix	417-428	12
β-strand	443-447	5	3
α-helix	450-453	4
α-helix	456-462	7

Chains B, F and H: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	4
β-strand	36-41	6	4
β-strand	47-55	9	4
α-helix	58-60	3
α-helix	68-75	8
β-strand	79	1	5
β-strand	80	1	6
β-strand	84	1	5
α-helix	85-94	10
β-strand	98-103	6	4
β-strand	107-115	9	4
α-helix	116-118	3
α-helix	119-131	13
β-strand	133	1	6
α-helix	137-154	18
α-helix	158-170	13
α-helix	175-177	3
α-helix	184-189	6
α-helix	192-202	11
α-helix	205-207	3
β-strand	208-214	7	4
α-helix	218-229	12
α-helix	233-235	3
α-helix	248-249	2
β-strand	254-259	6	7
β-strand	265-273	9	7
α-helix	282-292	11
β-strand	294-296	3	7
β-strand	300	1	7
α-helix	308-314	7
β-strand	322-329	8	7
β-strand	334-343	10	7
α-helix	349-364	16
α-helix	370-385	16
α-helix	391-405	15
α-helix	411-419	9
α-helix	423-433	11
β-strand	439-445	7	7
α-helix	447-449	3
α-helix	450-452	3
α-helix	453-461	9

Chain C: 29 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	20-23	4	8
β-strand	29-33	5	8
β-strand	40-46	7	8
α-helix	50-52	3
α-helix	60-67	8
β-strand	72	1	9
α-helix	77-86	10
β-strand	91-95	5	8
β-strand	100-106	7	8
α-helix	108-110	3
α-helix	111-123	13
β-strand	125	1	9
α-helix	129-146	18
α-helix	150-162	13
α-helix	167-169	3
α-helix	174-175	2
α-helix	176-181	6
α-helix	184-194	11
α-helix	197-199	3
β-strand	200-205	6	8
α-helix	209-220	12
α-helix	228-230	3
α-helix	233-235	3
β-strand	240-244	5	10
α-helix	245-248	4
α-helix	254-255	2
β-strand	257-264	8	10
α-helix	273-283	11
β-strand	285-287	3	10
α-helix	301	1
α-helix	302-307	6
β-strand	313-322	10	10
β-strand	327-335	9	10
α-helix	337-339	3
α-helix	340-352	13
α-helix	361-363	3
α-helix	364-381	18
α-helix	385-399	15
α-helix	405-413	9
α-helix	417-428	12
β-strand	443-447	5	10
α-helix	451-453	3
α-helix	456-462	7

Chain D: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	11
β-strand	36-41	6	11
β-strand	47-55	9	11
α-helix	58-60	3
α-helix	68-75	8
β-strand	79	1	12
β-strand	80	1	13
β-strand	84	1	12
α-helix	85-94	10
β-strand	98-103	6	11
β-strand	107-115	9	11
α-helix	116-118	3
α-helix	119-131	13
β-strand	133	1	13
α-helix	137-154	18
α-helix	158-170	13
α-helix	175-177	3
α-helix	184-189	6
α-helix	192-202	11
α-helix	205-207	3
β-strand	208-214	7	11
α-helix	218-229	12
α-helix	233-235	3
α-helix	248-249	2
β-strand	254-259	6	14
β-strand	265-273	9	14
α-helix	282-292	11
β-strand	295-296	2	14
β-strand	300	1	14
α-helix	308-314	7
β-strand	322-329	8	14
β-strand	334-343	10	14
α-helix	349-364	16
α-helix	370-385	16
α-helix	391-405	15
α-helix	411-419	9
α-helix	423-433	11
β-strand	439-445	7	14
α-helix	447-449	3
α-helix	450-452	3
α-helix	453-461	9

Chain G: 29 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	20-23	4	22
β-strand	29-33	5	22
β-strand	40-46	7	22
α-helix	50-52	3
α-helix	60-66	7
β-strand	72	1	23
α-helix	77-86	10
β-strand	91-95	5	22
β-strand	100-106	7	22
α-helix	108-110	3
α-helix	111-123	13
β-strand	125	1	23
α-helix	129-146	18
α-helix	150-162	13
α-helix	167-169	3
α-helix	174-175	2
α-helix	176-181	6
α-helix	184-194	11
α-helix	197-199	3
β-strand	200-205	6	22
α-helix	209-220	12
α-helix	228-230	3
α-helix	233-235	3
β-strand	240-244	5	24
α-helix	245-248	4
α-helix	254-255	2
β-strand	257-264	8	24
α-helix	273-283	11
β-strand	285-287	3	24
α-helix	301	1
α-helix	302-307	6
β-strand	313-322	10	24
β-strand	327-335	9	24
α-helix	337-339	3
α-helix	340-352	13
α-helix	361-363	3
α-helix	364-381	18
α-helix	385-399	15
α-helix	405-413	9
α-helix	417-428	12
β-strand	443-447	5	24
α-helix	451-453	3
α-helix	456-462	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitochondrial processing peptidase alpha subunit	A, C, E, G	protein	475	Saccharomyces cerevisiae	P11914 (AlphaFold model)
Mitochondrial processing peptidase beta subunit	B, D, F, H	protein	443	Saccharomyces cerevisiae	P10507 (AlphaFold model)

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

>1HR6_1 MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT (chains A, C, E, G)
ARTDNFKLSSLANGLKVATSNTPGHFSALGLYIDAGSRFEGRNLKGCTHILDRLAFKSTE
HVEGRAMAETLELLGGNYQCTSSRENLMYQASVFNQDVGKMLQLMSETVRFPKITEQELQ
EQKLSAEYEIDEVWMKPELVLPELLHTAAYSGETLGSPLICPRGLIPSISKYYLLDYRNK
FYTPENTVAAFVGVPHEKALELTGKYLGDWQSTHPPITKKVAQYTGGESCIPPAPVFGNL
PELFHIQIGFEGLPIDHPDIYALATLQTLLGGGGSFSAGGPGKGMYSRLYTHVLNQYYFV
ENCVAFNHSYSDSGIFGISLSCIPQAAPQAVEVIAQQMYNTFANKDLRLTEDEVSRAKNQ
LKSSLLMNLESKLVELEDMGRQVLMHGRKIPVNEMISKIEDLKPDDISRVAEMIFTGNVN
NAGNGKGRATVVMQGDRGSFGDVENVLKAYGLGNSSSSKNDSPKKKGWFHHHHHH

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

>1HR6_2 MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT (chains B, D, F, H)
ASQIPGTRTSKLPNGLTIATEYIPNTSSATVGIFVDAGSRAENVKNNGTAHFLEHLAFKG
TQNRPQQGIELEIENIGSHLNAYTSRENTVYYAKSLQEDIPKAVDILSDILTKSVLDNSA
IERERDVIIRESEEVDKMYDEVVFDHLHEITYKDQPLGRTILGPIKNIKSITRTDLKDYI
TKNYKGDRMVLAGAGAVDHEKLVQYAQKYFGHVPKSESPVPLGSPRGPLPVFCRGERFIK
ENTLPTTHIAIALEGVSWSAPDYFVALATQAIVGNWDRAIGTGTNSPSPLAVAASQNGSL
ANSYMSFSTSYADSGLWGMYIVTDSNEHNVRLIVNEILKEWKRIKSGKISDAEVNRAKAQ
LKAALLLSLDGSTAIVEDIGRQVVTTGKRLSPEEVFEQVDKITKDDIIMWANYRLQNKPV
SMVALGNTSTVPNVSYIEEKLNQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (EPE) are not listed.

Primary citation

Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences. Taylor, A.B., Smith, B.S., Kitada, S. et al. Structure (2001) 9:615-625. DOI 10.1016/S0969-2126(01)00621-9 · PubMed

Other PDB entries of the same protein (UniProt P11914 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1HR7 2.55 Å, Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant
1HR8 2.7 Å, Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Cytochrome C…
1HR9 3.01 Å, Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate…

Browse structure collections

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