1HR9: Mitochondrial processing peptidase alpha subunit
Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal Peptide. Determined by X-ray diffraction at 3.01 Å resolution. Released 11 Jul 2001.
- Method
- X-ray diffraction
- Resolution
- 3.01 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 12
- Atoms
- 27,925
- Mol. weight
- 410.06 kDa
- Ligands
- ZN
- Released
- 11 Jul 2001
Explore 1HR9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1HR9 contains 202 α-helices and 128 β-strands across 12 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: 27 helices, 14 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 |
| α-helix | 77-85 | 9 | |
| 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 | 176-178 | 3 | |
| 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 | 253-255 | 3 | |
| β-strand | 257-264 | 8 | 3 |
| α-helix | 273-283 | 11 | |
| β-strand | 285-286 | 2 | 3 |
| α-helix | 301 | 1 | |
| α-helix | 302-307 | 6 | |
| β-strand | 313-322 | 10 | 3 |
| β-strand | 327-335 | 9 | 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 | 451-453 | 3 | |
| α-helix | 456-462 | 7 | |
Chains B and H: 23 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-30 | 5 | 4 |
| β-strand | 36-41 | 6 | 4 |
| β-strand | 47-54 | 8 | 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 | 85-95 | 11 | |
| β-strand | 98-104 | 7 | 4 |
| β-strand | 108-115 | 8 | 4 |
| α-helix | 116-118 | 3 | |
| α-helix | 119-130 | 12 | |
| β-strand | 133 | 1 | 6 |
| α-helix | 139-154 | 16 | |
| α-helix | 158-170 | 13 | |
| 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 | 232-235 | 4 | |
| α-helix | 248-249 | 2 | |
| β-strand | 255-259 | 5 | 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 | 370-381 | 12 | |
| α-helix | 382-386 | 5 | |
| 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 | 453-461 | 9 | |
Chain C: 27 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 | 60-66 | 7 | |
| β-strand | 72 | 1 | 9 |
| α-helix | 77-85 | 9 | |
| 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 | 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 | 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 | 450-453 | 4 | |
| α-helix | 456-462 | 7 | |
Chain D: 24 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-30 | 5 | 11 |
| β-strand | 36-41 | 6 | 11 |
| β-strand | 47-54 | 8 | 11 |
| α-helix | 58-60 | 3 | |
| α-helix | 68-75 | 8 | |
| α-helix | 76-78 | 3 | |
| β-strand | 79 | 1 | 12 |
| β-strand | 80 | 1 | 13 |
| β-strand | 84 | 1 | 12 |
| α-helix | 85-95 | 11 | |
| β-strand | 98-104 | 7 | 11 |
| β-strand | 108-115 | 8 | 11 |
| α-helix | 116-118 | 3 | |
| α-helix | 119-130 | 12 | |
| β-strand | 133 | 1 | 13 |
| α-helix | 139-154 | 16 | |
| α-helix | 158-170 | 13 | |
| 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 | 255-259 | 5 | 14 |
| β-strand | 265-273 | 9 | 14 |
| α-helix | 282-292 | 11 | |
| β-strand | 294-296 | 3 | 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 | 370-381 | 12 | |
| α-helix | 382-386 | 5 | |
| 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 | 453-461 | 9 | |
Chain E: 28 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-23 | 4 | 15 |
| β-strand | 29-33 | 5 | 15 |
| β-strand | 40-46 | 7 | 15 |
| α-helix | 50-52 | 3 | |
| α-helix | 60-66 | 7 | |
| β-strand | 72 | 1 | 16 |
| α-helix | 77-85 | 9 | |
| β-strand | 91-95 | 5 | 15 |
| β-strand | 100-106 | 7 | 15 |
| α-helix | 108-110 | 3 | |
| α-helix | 111-123 | 13 | |
| β-strand | 125 | 1 | 16 |
| α-helix | 129-146 | 18 | |
| α-helix | 150-162 | 13 | |
| α-helix | 167-169 | 3 | |
| α-helix | 176-178 | 3 | |
| α-helix | 184-194 | 11 | |
| α-helix | 197-199 | 3 | |
| β-strand | 200-205 | 6 | 15 |
| α-helix | 209-220 | 12 | |
| α-helix | 228-230 | 3 | |
| α-helix | 233-235 | 3 | |
| β-strand | 240-244 | 5 | 17 |
| α-helix | 245-248 | 4 | |
| α-helix | 254-255 | 2 | |
| β-strand | 257-264 | 8 | 17 |
| α-helix | 273-283 | 11 | |
| β-strand | 285-287 | 3 | 17 |
| α-helix | 301 | 1 | |
| α-helix | 302-307 | 6 | |
| β-strand | 313-322 | 10 | 17 |
| β-strand | 327-335 | 9 | 17 |
| 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 | 17 |
| α-helix | 451-453 | 3 | |
| α-helix | 456-462 | 7 | |
Chain F: 22 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-30 | 5 | 18 |
| β-strand | 36-41 | 6 | 18 |
| β-strand | 47-54 | 8 | 18 |
| α-helix | 58-60 | 3 | |
| α-helix | 68-75 | 8 | |
| β-strand | 79 | 1 | 19 |
| β-strand | 80 | 1 | 20 |
| β-strand | 84 | 1 | 19 |
| α-helix | 85-95 | 11 | |
| β-strand | 98-104 | 7 | 18 |
| β-strand | 108-115 | 8 | 18 |
| α-helix | 116-118 | 3 | |
| α-helix | 119-130 | 12 | |
| β-strand | 133 | 1 | 20 |
| α-helix | 139-154 | 16 | |
| α-helix | 158-170 | 13 | |
| α-helix | 184-189 | 6 | |
| α-helix | 192-202 | 11 | |
| α-helix | 205-207 | 3 | |
| β-strand | 208-214 | 7 | 18 |
| α-helix | 218-229 | 12 | |
| α-helix | 248-249 | 2 | |
| β-strand | 255-259 | 5 | 21 |
| β-strand | 265-273 | 9 | 21 |
| α-helix | 282-292 | 11 | |
| β-strand | 294-296 | 3 | 21 |
| β-strand | 300 | 1 | 21 |
| α-helix | 308-314 | 7 | |
| β-strand | 322-329 | 8 | 21 |
| β-strand | 334-343 | 10 | 21 |
| α-helix | 349-364 | 16 | |
| α-helix | 370-381 | 12 | |
| α-helix | 382-386 | 5 | |
| α-helix | 391-405 | 15 | |
| α-helix | 411-419 | 9 | |
| α-helix | 423-433 | 11 | |
| β-strand | 439-445 | 7 | 21 |
| α-helix | 447-449 | 3 | |
| α-helix | 453-461 | 9 | |
Chain G: 27 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 | 176-178 | 3 | |
| 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 | 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 | |
Chains O, P and R: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-8 | 2 | 4 |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
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) |
| Malate dehydrogenase | O, P, Q, R | protein | 8 | | P17505 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>1HR9_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
>1HR9_2 MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT (chains B, D, F, H)
ASQIPGTRTSKLPNGLTIATEYIPNTSSATVGIFVDAGSRAENVKNNGTAHFLQHLAFKG
TQNRPQQGIELEIENIGSHLNAYTSRENTVYYAKSLQEDIPKAVDILSDILTKSVLDNSA
IERERDVIIRESEEVDKMYDEVVFDHLHEITYKDQPLGRTILGPIKNIKSITRTDLKDYI
TKNYKGDRMVLAGAGAVDHEKLVQYAQKYFGHVPKSESPVPLGSPRGPLPVFCRGERFIK
ENTLPTTHIAIALEGVSWSAPDYFVALATQAIVGNWDRAIGTGTNSPSPLAVAASQNGSL
ANSYMSFSTSYADSGLWGMYIVTDSNEHNVRLIVNEILKEWKRIKSGKISDAEVNRAKAQ
LKAALLLSLDGSTAIVEDIGRQVVTTGKRLSPEEVFEQVDKITKDDIIMWANYRLQNKPV
SMVALGNTSTVPNVSYIEEKLNQ
Sequence of entity 3 (O, P, Q, R), FASTA
>1HR9_3 MALATE DEHYDROGENASE (chains O, P, Q, R)
LSRVAKRA
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:
- 1HR6 2.5 Å, Yeast Mitochondrial Processing Peptidase
- 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…
Browse structure collections
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