6YMY: Cytochrome c oxidase subunit 1
Cytochrome c oxidase from Saccharomyces cerevisiae. Determined by electron microscopy at 3.41 Å resolution. Released 9 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 3.41 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 12
- Atoms
- 14,612
- Mol. weight
- 209.31 kDa
- Ligands
- CU, HEA, PTY, CN3
- Released
- 9 Sept 2020
Explore 6YMY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6YMY contains 90 α-helices and 23 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: 30 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-39 | 26 | |
| α-helix | 57-66 | 10 | |
| α-helix | 67-71 | 5 | |
| α-helix | 72 | 1 | |
| α-helix | 73-78 | 6 | |
| α-helix | 79-87 | 9 | |
| α-helix | 96-118 | 23 | |
| α-helix | 131-134 | 4 | |
| α-helix | 143-166 | 24 | |
| α-helix | 184-195 | 12 | |
| α-helix | 200-215 | 16 | |
| α-helix | 230-246 | 17 | |
| α-helix | 249-262 | 14 | |
| α-helix | 270-281 | 12 | |
| α-helix | 289-291 | 3 | |
| α-helix | 299-305 | 7 | |
| α-helix | 313-329 | 17 | |
| α-helix | 336-359 | 24 | |
| α-helix | 364-366 | 3 | |
| β-strand | 370 | 1 | 1 |
| α-helix | 371-377 | 7 | |
| α-helix | 387-400 | 14 | |
| α-helix | 407-425 | 19 | |
| α-helix | 428-434 | 7 | |
| α-helix | 436 | 1 | |
| β-strand | 437 | 1 | 1 |
| α-helix | 445-447 | 3 | |
| α-helix | 450-476 | 27 | |
| α-helix | 481-483 | 3 | |
| α-helix | 501-504 | 4 | |
| α-helix | 514-516 | 3 | |
| α-helix | 522-523 | 2 | |
| β-strand | 532-533 | 2 | 2 |
Chain b: 5 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-64 | 34 | |
| α-helix | 79-82 | 4 | |
| α-helix | 84-105 | 22 | |
| β-strand | 115-121 | 7 | 3 |
| β-strand | 126-130 | 5 | 3 |
| β-strand | 141-145 | 5 | 3 |
| β-strand | 147 | 1 | 4 |
| β-strand | 163 | 1 | 4 |
| β-strand | 167-169 | 3 | 5 |
| β-strand | 175-181 | 7 | 3 |
| β-strand | 188-190 | 3 | 6 |
| β-strand | 195-197 | 3 | 6 |
| β-strand | 205-208 | 4 | 3 |
| β-strand | 215-217 | 3 | 5 |
| β-strand | 220 | 1 | 6 |
| β-strand | 236-238 | 3 | 5 |
| α-helix | 241-250 | 10 | |
Chain c: 18 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 17-19 | 3 | |
| α-helix | 22-25 | 4 | |
| α-helix | 27-40 | 14 | |
| α-helix | 50-63 | 14 | |
| α-helix | 65-74 | 10 | |
| α-helix | 81-100 | 20 | |
| α-helix | 104-111 | 8 | |
| α-helix | 126 | 1 | |
| α-helix | 131-133 | 3 | |
| α-helix | 137-148 | 12 | |
| α-helix | 157-161 | 5 | |
| α-helix | 164-175 | 12 | |
| α-helix | 177-187 | 11 | |
| α-helix | 205-208 | 4 | |
| α-helix | 210-231 | 22 | |
| α-helix | 241-261 | 21 | |
| α-helix | 262-267 | 6 | |
Chain d: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 43-45 | 3 | |
| α-helix | 50-52 | 3 | |
| α-helix | 67-75 | 9 | |
| β-strand | 98-99 | 2 | 7 |
| β-strand | 109-110 | 2 | 2 |
| β-strand | 123-124 | 2 | 2 |
| β-strand | 127 | 1 | 8 |
| β-strand | 130 | 1 | 8 |
| β-strand | 132 | 1 | 7 |
| β-strand | 141-142 | 2 | 7 |
Chain e: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-31 | 4 | |
| α-helix | 43-46 | 4 | |
| α-helix | 49-56 | 8 | |
| α-helix | 66-77 | 12 | |
| α-helix | 92-115 | 24 | |
| α-helix | 118-121 | 4 | |
| α-helix | 132-139 | 8 | |
Chain f: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-59 | 10 | |
| α-helix | 67-77 | 11 | |
| α-helix | 82-84 | 3 | |
| α-helix | 85-96 | 12 | |
| α-helix | 102-113 | 12 | |
| α-helix | 118-127 | 10 | |
| α-helix | 131-135 | 5 | |
| α-helix | 137-139 | 3 | |
| α-helix | 140-143 | 4 | |
Chain g: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-12 | 7 | |
| α-helix | 19-21 | 3 | |
| α-helix | 24-26 | 3 | |
| α-helix | 27-40 | 14 | |
| α-helix | 43-46 | 4 | |
| α-helix | 48-53 | 6 | |
Chain h: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 49-57 | 9 | |
| α-helix | 59-74 | 16 | |
4 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 | 530 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P00401 (AlphaFold model) |
| Cytochrome c oxidase subunit 2 | b | protein | 236 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P00410 (AlphaFold model) |
| Cytochrome c oxidase subunit 3 | c | protein | 268 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P00420 (AlphaFold model) |
| Cytochrome c oxidase subunit 4, mitochondrial | d | protein | 117 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P04037 (AlphaFold model) |
| Cytochrome c oxidase subunit 5A, mitochondrial | e | protein | 128 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P00424 |
| Cytochrome c oxidase subunit 6, mitochondrial | f | protein | 99 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P00427 |
| Cytochrome c oxidase subunit 7, mitochondrial | g | protein | 55 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P10174 |
| Cytochrome c oxidase subunit 8, mitochondrial | h | protein | 51 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P04039 |
| Cytochrome c oxidase subunit 9, mitochondrial | i | protein | 52 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P07255 |
| Cytochrome c oxidase subunit 12, mitochondrial | j | protein | 78 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q01519 |
| Cytochrome c oxidase subunit 13, mitochondrial | k | protein | 114 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32799 |
| Cytochrome c oxidase subunit 26, mitochondrial | m | protein | 38 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q2V2P9 |
Sequence of entity 1 (a), FASTA
>6YMY_1 Cytochrome c oxidase subunit 1 (chains a)
WLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVVGHAV
LMIFFLVMPALIGGFGNYLLPLMIGATDTAFPRINNIAFWVLPMGLVCLVTSTLVESGAG
TGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMHKLPL
FVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFGHPEV
YILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDADTRAY
FTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALANASLD
VAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIGANVI
FFPMHFLGINGMPRRIPDYPDAFAGWNYVASIGSFIATLSLFLFIYILYDQLVNGLNNKV
NNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS
Sequence of entity 2 (b), FASTA
>6YMY_2 Cytochrome c oxidase subunit 2 (chains b)
DVPTPYACYFQDSATPNQEGILELHDNIMFYLLVILGLVSWMLYTIVMTYSKNPIAYKYI
KHGQTIEVIWTIFPAVILLIIAFPSFILLYLCDEVISPAMTIKAIGYQWYWKYEYSDFIN
DSGETVEFESYVIPDELLEEGQLRLLDTDTSMVVPVDTHIRFVVTAADVIHDFAIPSLGI
KVDATPGRLNQVSALIQREGVFYGACSELCGTGHANMPIKIEAVSLPKFLEWLNEQ
Sequence of entity 3 (c), FASTA
>6YMY_3 Cytochrome c oxidase subunit 3 (chains c)
THLERSRHQQHPFHMVMPSPWPIVVSFALLSLALSTALTMHGYIGNMNMVYLALFVLLTS
SILWFRDIVAEATYLGDHTMAVRKGINLGFLMFVLSEVLIFAGLFWAYFHSAMSPDVTLG
ACWPPVGIEAVQPTELPLLNTIILLSSGATVTYSHHALIAGNRNKALSGLLITFWLIVIF
VTCQYIEYTNAAFTISDGVYGSVFYAGTGLHFLHMVMLAAMLGVNYWRMRNYHLTAGHHV
GYETTIIYTHVLDVIWLFLYVVFYWWGV
Sequence of entity 4 (d), FASTA
>6YMY_4 Cytochrome c oxidase subunit 4, mitochondrial (chains d)
VVKTAQNLAEVNGPETLIGPGAKEGTVPTDLDQETGLARLELLGKLEGIDVFDTKPLDSS
RKGTMKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNPV
Sequence of entity 5 (e), FASTA
>6YMY_5 Cytochrome c oxidase subunit 5A, mitochondrial (chains e)
ALSNAAVMDLQSRWENMPSTEQQDIVSKLSERQKLPWAQLTEPEKQAVWYISYGEWGPRR
PVLNKGDSSFIAKGVAAGLLFSVGLFAVVRMAGGQDAKTMNKEWQLKSDEYLKSKNANPW
GGYSQVQS
Sequence of entity 6 (f), FASTA
>6YMY_6 Cytochrome c oxidase subunit 6, mitochondrial (chains f)
ETFEEFTARYEKEFDEAYDLFEVQRVLNNCFSYDLVPAPAVIEKALRAARRVNDLPTAIR
VFEALKYKVENEDQYKAYLDELKDVRQELGVPLKEELFP
Sequence of entity 7 (g), FASTA
>6YMY_7 Cytochrome c oxidase subunit 7, mitochondrial (chains g)
NKVIQLQKIFQSSTKPLWWRHPRSALYLYPFYAIFAVAVVTPLLYIPNAIRGIKA
Sequence of entity 8 (h), FASTA
>6YMY_8 Cytochrome c oxidase subunit 8, mitochondrial (chains h)
VHFKDGVYENIPFKVKGRKTPYALSHFGFFAIGFAVPFVACYVQLKKSGAF
Sequence of entity 9 (i), FASTA
>6YMY_9 Cytochrome c oxidase subunit 9, mitochondrial (chains i)
TIAPITGTIKRRVIMDIVLGFSLGGVMASYWWWGFHMDKINKREKFYAELAE
Sequence of entity 10 (j), FASTA
>6YMY_10 Cytochrome c oxidase subunit 12, mitochondrial (chains j)
NSPLHTVGFDARFPQQNQTKHCWQSYVDYHKCVNMKGEDFAPCKVFWKTYNALCPLDWIE
KWDDQREKGIFAGDINSD
Sequence of entity 11 (k), FASTA
>6YMY_11 Cytochrome c oxidase subunit 13, mitochondrial (chains k)
NALKPAFGPPDKVAAQKFKESLMATEKHAKDTSNMWVKISVWVALPAIALTAVNTYFVEK
EHAEHREHLKHVPDSEWPRDYEFMNIRSKPFFWGDGDKTLFWNPVVNRHIEHDD
Sequence of entity 12 (m), FASTA
>6YMY_12 Cytochrome c oxidase subunit 26, mitochondrial (chains m)
ESWVITEGRRLIPEIFQWSAVLSVCLGWPGAVYFFSKA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CU | Copper (II) ion | Cu | 1 |
| HEA | Heme-a | C49 H56 Fe N4 O6 | 2 |
| PTY | Phosphatidylethanolamine | C40 H80 N O8 P | 7 |
| CN3 | (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(prop… | C36 H68 O17 P2 | 1 |
| CUA | Dinuclear copper ion | Cu2 | 1 |
| PCF | 1,2-diacyl-sn-glycero-3-phoshocholine | C40 H80 N O8 P | 3 |
| ZN | Zinc ion | Zn | 1 |
Primary citation
Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance. Berndtsson, J., Aufschnaiter, A., Rathore, S. et al. EMBO Rep (2020) 21:e51015-e51015. DOI 10.15252/embr.202051015 · 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
- 7Z10 3.87 Å, Monomeric respiratory complex IV isolated from S. cerevisiae
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