7Z10: Cytochrome c oxidase subunit 1
Monomeric respiratory complex IV isolated from S. cerevisiae. Determined by electron microscopy at 3.87 Å resolution. Released 3 Aug 2022.
- Method
- Electron microscopy
- Resolution
- 3.87 Å
- Organism
- Saccharomyces cerevisiae S288C
- Chains
- 9
- Atoms
- 12,574
- Mol. weight
- 178.88 kDa
- Ligands
- HEA, MG, ZN, CUA
- Released
- 3 Aug 2022
Explore 7Z10 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7Z10 contains 73 α-helices and 28 β-strands across 9 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, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 11-39 | 29 | |
| α-helix | 52-64 | 13 | |
| α-helix | 65-69 | 5 | |
| α-helix | 71 | 1 | |
| α-helix | 72-80 | 9 | |
| α-helix | 81-87 | 7 | |
| α-helix | 96-118 | 23 | |
| α-helix | 143-171 | 29 | |
| α-helix | 179-181 | 3 | |
| α-helix | 184-215 | 32 | |
| α-helix | 229-262 | 34 | |
| α-helix | 270-283 | 14 | |
| α-helix | 288-292 | 5 | |
| α-helix | 299-311 | 13 | |
| α-helix | 313-327 | 15 | |
| α-helix | 336-358 | 23 | |
| α-helix | 361-364 | 4 | |
| β-strand | 370 | 1 | 1 |
| α-helix | 371-377 | 7 | |
| α-helix | 378-387 | 10 | |
| α-helix | 388-400 | 13 | |
| α-helix | 407-425 | 19 | |
| α-helix | 427-433 | 7 | |
| β-strand | 437 | 1 | 1 |
| α-helix | 450-484 | 35 | |
| α-helix | 494-495 | 2 | |
| α-helix | 502-506 | 5 | |
| α-helix | 519 | 1 | |
| β-strand | 533 | 1 | 2 |
Chain b: 8 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-19 | 2 | |
| α-helix | 31-65 | 35 | |
| α-helix | 79-106 | 28 | |
| β-strand | 115-122 | 8 | 3 |
| β-strand | 125-134 | 10 | 3 |
| β-strand | 140-145 | 6 | 3 |
| α-helix | 146 | 1 | |
| β-strand | 147 | 1 | 4 |
| α-helix | 148-149 | 2 | |
| α-helix | 150-152 | 3 | |
| β-strand | 155 | 1 | 5 |
| β-strand | 157 | 1 | 5 |
| α-helix | 158 | 1 | |
| β-strand | 163 | 1 | 4 |
| β-strand | 167-170 | 4 | 6 |
| β-strand | 175-181 | 7 | 3 |
| β-strand | 186-190 | 5 | 7 |
| β-strand | 195-199 | 5 | 7 |
| β-strand | 205-209 | 5 | 3 |
| β-strand | 215-220 | 6 | 6 |
| β-strand | 225 | 1 | 8 |
| β-strand | 227 | 1 | 8 |
| β-strand | 233-239 | 7 | 6 |
| α-helix | 241-250 | 10 | |
Chain c: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 17-19 | 3 | |
| α-helix | 22-40 | 19 | |
| α-helix | 50-71 | 22 | |
| α-helix | 72-76 | 5 | |
| α-helix | 81-113 | 33 | |
| α-helix | 137-161 | 25 | |
| α-helix | 164-190 | 27 | |
| α-helix | 199-231 | 33 | |
| α-helix | 242-265 | 24 | |
Chain d: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 43-45 | 3 | |
| α-helix | 56-58 | 3 | |
| α-helix | 59-62 | 4 | |
| α-helix | 65-75 | 11 | |
| α-helix | 84-86 | 3 | |
| β-strand | 98-102 | 5 | 9 |
| β-strand | 106 | 1 | 10 |
| β-strand | 109-111 | 3 | 2 |
| β-strand | 122-124 | 3 | 2 |
| β-strand | 127 | 1 | 10 |
| β-strand | 132-133 | 2 | 9 |
| β-strand | 140-145 | 6 | 9 |
Chain e: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-31 | 4 | |
| α-helix | 43-56 | 14 | |
| α-helix | 66-77 | 12 | |
| α-helix | 81-83 | 3 | |
| α-helix | 91-115 | 25 | |
| α-helix | 118-121 | 4 | |
| α-helix | 127-138 | 12 | |
Chain f: 7 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 49-62 | 14 | |
| α-helix | 66-77 | 12 | |
| β-strand | 81 | 1 | 11 |
| α-helix | 82-84 | 3 | |
| α-helix | 85-96 | 12 | |
| α-helix | 103-114 | 12 | |
| α-helix | 118-125 | 8 | |
| α-helix | 129-135 | 7 | |
Chain g: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-13 | 9 | |
| α-helix | 19-21 | 3 | |
| α-helix | 26-42 | 17 | |
| α-helix | 44-47 | 4 | |
| α-helix | 48-52 | 5 | |
Chain h: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-73 | 24 | |
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 |
|---|
| Cytochrome c oxidase subunit 1 | a | protein | 534 | Saccharomyces cerevisiae S288C | P00401 (AlphaFold model) |
| Cytochrome c oxidase subunit 2 | b | protein | 236 | Saccharomyces cerevisiae S288C | P00410 (AlphaFold model) |
| Cytochrome C oxidase subunit 3; synonym: cytochrome C oxidase polypeptide III, COX3 | c | protein | 269 | Saccharomyces cerevisiae S288C | P00420 (AlphaFold model) |
| Cytochrome c oxidase subunit 4, mitochondrial | d | protein | 121 | Saccharomyces cerevisiae S288C | P04037 (AlphaFold model) |
| Cytochrome c oxidase polypeptide 5A, mitochondrial | e | protein | 133 | Saccharomyces cerevisiae S288C | P00424 |
| Cytochrome c oxidase subunit 6, mitochondrial | f | protein | 104 | Saccharomyces cerevisiae S288C | P00427 |
| Cytochrome C oxidase subunit 7; synonym: cytochrome C oxidase polypeptide VII, COX7 | g | protein | 59 | Saccharomyces cerevisiae S288C | P10174 |
| Cytochrome c oxidase polypeptide VIII, mitochondrial | h | protein | 47 | Saccharomyces cerevisiae S288C | P04039 |
| Cytochrome C oxidase subunit 7A; synonym: cytochrome C oxidase polypeptide viia, COX9 | i | protein | 55 | Saccharomyces cerevisiae S288C | P07255 |
Sequence of entity 1 (a), FASTA
>7Z10_1 Cytochrome c oxidase subunit 1 (chains a)
MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVV
GHAVLMIFFLVMPALIGGFGNYLLPLMIGATDTAFPRINNIAFWVLPMGLVCLVTSTLVE
SGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMH
KLPLFVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFG
HPEVYILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDAD
TRAYFTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALAN
ASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIG
ANVIFFPMHFLGINGMPRRIPDYPDAFAGWNYVASIGSFIATLSLFLFIYILYDQLVNGL
NNKVNNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS
Sequence of entity 2 (b), FASTA
>7Z10_2 Cytochrome c oxidase subunit 2 (chains b)
DVPTPYACYFQDSATPNQEGILELHDNIMFYLLVILGLVSWMLYTIVMTYSKNPIAYKYI
KHGQTIEVIWTIFPAVILLIIAFPSFILLYLCDEVISPAMTIKAIGYQWYWKYEYSDFIN
DSGETVEFESYVIPDELLEEGQLRLLDTDTSMVVPVDTHIRFVVTAADVIHDFAIPSLGI
KVDATPGRLNQVSALIQREGVFYGACSELCGTGHANMPIKIEAVSLPKFLEWLNEQ
Sequence of entity 3 (c), FASTA
>7Z10_3 CYTOCHROME C OXIDASE SUBUNIT 3; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE III, COX3 (chains c)
MTHLERSRHQQHPFHMVMPSPWPIVVSFALLSLALSTALTMHGYIGNMNMVYLALFVLLT
SSILWFRDIVAEATYLGDHTMAVRKGINLGFLMFVLSEVLIFAGLFWAYFHSAMSPDVTL
GACWPPVGIEAVQPTELPLLNTIILLSSGATVTYSHHALIAGNRNKALSGLLITFWLIVI
FVTCQYIEYTNAAFTISDGVYGSVFYAGTGLHFLHMVMLAAMLGVNYWRMRNYHLTAGHH
VGYETTIIYTHVLDVIWLFLYVVFYWWGV
Sequence of entity 4 (d), FASTA
>7Z10_4 Cytochrome c oxidase subunit 4, mitochondrial (chains d)
PVVKTAQNLAEVNGPETLIGPGAKEGTVPTDLDQETGLARLELLGKLEGIDVFDTKPLDS
SRKGTMKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNPVGV
P
Sequence of entity 5 (e), FASTA
>7Z10_5 Cytochrome c oxidase polypeptide 5A, mitochondrial (chains e)
AQTHALSNAAVMDLQSRWENMPSTEQQDIVSKLSERQKLPWAQLTEPEKQAVWYISYGEW
GPRRPVLNKGDSSFIAKGVAAGLLFSVGLFAVVRMAGGQDAKTMNKEWQLKSDEYLKSKN
ANPWGGYSQVQSK
Sequence of entity 6 (f), FASTA
>7Z10_6 Cytochrome c oxidase subunit 6, mitochondrial (chains f)
DEETFEEFTARYEKEFDEAYDLFEVQRVLNNCFSYDLVPAPAVIEKALRAARRVNDLPTA
IRVFEALKYKVENEDQYKAYLDELKDVRQELGVPLKEELFPSSS
Sequence of entity 7 (g), FASTA
>7Z10_7 CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VII, COX7 (chains g)
ANKVIQLQKIFQSSTKPLWWRHPRSALYLYPFYAIFAVAVVTPLLYIPNAIRGIKAKKA
Sequence of entity 8 (h), FASTA
>7Z10_8 Cytochrome c oxidase polypeptide VIII, mitochondrial (chains h)
VHFKDGVYENIPFKVKGRKTPYALSHFGFFAIGFAVPFVACYVQLKK
Sequence of entity 9 (i), FASTA
>7Z10_9 CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIIA, COX9 (chains i)
TIAPITGTIKRRVIMDIVLGFSLGGVMASYWWWGFHMDKINKREKFYAELAERKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| HEA | Heme-a | C49 H56 Fe N4 O6 | 2 |
| MG | Magnesium ion | Mg | 1 |
| ZN | Zinc ion | Zn | 1 |
| CUA | Dinuclear copper ion | Cu2 | 1 |
| PEF | Di-palmitoyl-3-sn-phosphatidylethanolamine | C37 H74 N O8 P | 3 |
| CU | Copper (II) ion | Cu | 1 |
Primary citation
Cryo-EM structure of a monomeric yeast S. cerevisiae complex IV isolated with maltosides: Implications in supercomplex formation. Ing, G., Hartley, A.M., Pinotsis, N. et al. Biochim Biophys Acta Bioenerg (2022) 1863:148591-148591. DOI 10.1016/j.bbabio.2022.148591 · PubMed
Other PDB entries of the same protein (UniProt P00401 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9ETZ 2.4 Å, III2IV respiratory supercomplex from Saccharomyces cerevisiae
- 9BPB 2.57 Å, Tethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae
- 6T0B 2.8 Å, The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae
- 8DH6 2.94 Å, Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV)…
- 6YMX 3.17 Å, CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae
- 8E7S 3.2 Å, III2IV2 respiratory supercomplex from Saccharomyces cerevisiae with 4 bound UQ6
- 6GIQ 3.23 Å, Saccharomyces cerevisiae respiratory supercomplex III2IV
- 6T15 3.29 Å, The III2-IV(5B)1 respiratory supercomplex from S. cerevisiae
- 8EC0 3.3 Å, III2IV respiratory supercomplex from Saccharomyces cerevisiae cardiolipin-lacking mutant
- 6HU9 3.35 Å, III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae
- 6YMY 3.41 Å, Cytochrome c oxidase from Saccharomyces cerevisiae
Browse structure collections
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