8DH6: Cytochrome c oxidase subunit 1
Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs. Determined by electron microscopy at 2.94 Å resolution. Released 20 Jul 2022.
- Method
- Electron microscopy
- Resolution
- 2.94 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 9
- Atoms
- 12,901
- Mol. weight
- 185.62 kDa
- Ligands
- CU, ZN, PEF, HEA
- Released
- 20 Jul 2022
Explore 8DH6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8DH6 contains 85 α-helices and 26 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: 29 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 11-39 | 29 | |
| α-helix | 52-66 | 15 | |
| α-helix | 67-71 | 5 | |
| α-helix | 72 | 1 | |
| α-helix | 73-79 | 7 | |
| α-helix | 80-87 | 8 | |
| 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 | 270-284 | 15 | |
| α-helix | 288-291 | 4 | |
| α-helix | 299-311 | 13 | |
| α-helix | 313-327 | 15 | |
| α-helix | 336-358 | 23 | |
| α-helix | 363-367 | 5 | |
| β-strand | 370 | 1 | 1 |
| α-helix | 371-378 | 8 | |
| α-helix | 379-387 | 9 | |
| α-helix | 388-401 | 14 | |
| α-helix | 407-425 | 19 | |
| α-helix | 427-434 | 8 | |
| α-helix | 436 | 1 | |
| β-strand | 437 | 1 | 1 |
| α-helix | 448-484 | 37 | |
| α-helix | 494-496 | 3 | |
| α-helix | 501-505 | 5 | |
| α-helix | 514-517 | 4 | |
| α-helix | 530-531 | 2 | |
| β-strand | 532-533 | 2 | 2 |
Chain b: 10 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-65 | 35 | |
| α-helix | 79-107 | 29 | |
| β-strand | 115-122 | 8 | 3 |
| β-strand | 125-130 | 6 | 3 |
| α-helix | 139-140 | 2 | |
| β-strand | 141-145 | 5 | 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 | 174-181 | 8 | 3 |
| β-strand | 188-190 | 3 | 6 |
| β-strand | 195-197 | 3 | 6 |
| β-strand | 205-210 | 6 | 3 |
| β-strand | 215-221 | 7 | 6 |
| α-helix | 227-229 | 3 | |
| β-strand | 233-239 | 7 | 6 |
| α-helix | 241-250 | 10 | |
Chain c: 14 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 | 49-70 | 22 | |
| α-helix | 71-75 | 5 | |
| α-helix | 81-114 | 34 | |
| α-helix | 118-120 | 3 | |
| α-helix | 126 | 1 | |
| α-helix | 130-133 | 4 | |
| α-helix | 137-161 | 25 | |
| α-helix | 164-190 | 27 | |
| α-helix | 199-231 | 33 | |
| α-helix | 242-261 | 20 | |
| α-helix | 262-267 | 6 | |
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 | 65-76 | 12 | |
| α-helix | 97 | 1 | |
| β-strand | 98-102 | 5 | 7 |
| β-strand | 106 | 1 | 8 |
| β-strand | 109-111 | 3 | 2 |
| β-strand | 122-124 | 3 | 2 |
| β-strand | 127 | 1 | 8 |
| β-strand | 132-133 | 2 | 7 |
| β-strand | 140-145 | 6 | 7 |
Chain e: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-31 | 4 | |
| α-helix | 34-37 | 4 | |
| α-helix | 43-57 | 15 | |
| α-helix | 61-63 | 3 | |
| α-helix | 66-77 | 12 | |
| α-helix | 81-83 | 3 | |
| α-helix | 91-115 | 25 | |
| α-helix | 119-121 | 3 | |
| α-helix | 126-138 | 13 | |
Chain f: 9 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 49-61 | 13 | |
| α-helix | 66-77 | 12 | |
| β-strand | 81 | 1 | 9 |
| α-helix | 82-84 | 3 | |
| α-helix | 85-97 | 13 | |
| α-helix | 101-114 | 14 | |
| α-helix | 118-127 | 10 | |
| α-helix | 129-135 | 7 | |
| α-helix | 137-139 | 3 | |
| α-helix | 140-143 | 4 | |
Chain g: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-13 | 9 | |
| α-helix | 19-21 | 3 | |
| α-helix | 27-46 | 20 | |
| α-helix | 48-53 | 6 | |
| α-helix | 55-58 | 4 | |
Chain h: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 49-73 | 25 | |
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 | P00401 (AlphaFold model) |
| Cytochrome c oxidase subunit 2 | b | protein | 236 | Saccharomyces cerevisiae | P00410 (AlphaFold model) |
| Cytochrome c oxidase subunit 3 | c | protein | 269 | Saccharomyces cerevisiae | P00420 (AlphaFold model) |
| Cytochrome c oxidase subunit 4, mitochondrial | d | protein | 130 | Saccharomyces cerevisiae | P04037 (AlphaFold model) |
| Cytochrome c oxidase subunit 5A, mitochondrial | e | protein | 133 | Saccharomyces cerevisiae | P00424 |
| Cytochrome c oxidase subunit 6, mitochondrial | f | protein | 108 | Saccharomyces cerevisiae | P00427 |
| Cytochrome c oxidase subunit 7, mitochondrial | g | protein | 59 | Saccharomyces cerevisiae | P10174 |
| Cytochrome c oxidase subunit 8, mitochondrial | h | protein | 51 | Saccharomyces cerevisiae | P04039 |
| Cytochrome c oxidase subunit 9, mitochondrial | i | protein | 55 | Saccharomyces cerevisiae | P07255 |
Sequence of entity 1 (a), FASTA
>8DH6_1 Cytochrome c oxidase subunit 1 (chains a)
MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVV
GHAVLMIFFLVMPALIGGFGNYLLPLMIGATDTAFPRINNIAFWVLPMGLVCLVTSTLVE
SGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMH
KLPLFVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFG
HPEVYILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDAD
TRAYFTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALAN
ASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIG
ANVIFFPMHFLGINGMPRRIPDYPDAFAGWNYVASIGSFIATLSLFLFIYILYDQLVNGL
NNKVNNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS
Sequence of entity 2 (b), FASTA
>8DH6_2 Cytochrome c oxidase subunit 2 (chains b)
DVPTPYACYFQDSATPNQEGILELHDNIMFYLLVILGLVSWMLYTIVMTYSKNPIAYKYI
KHGQTIEVIWTIFPAVILLIIAFPSFILLYLCDEVISPAMTIKAIGYQWYWKYEYSDFIN
DSGETVEFESYVIPDELLEEGQLRLLDTDTSMVVPVDTHIRFVVTAADVIHDFAIPSLGI
KVDATPGRLNQVSALIQREGVFYGACSELCGTGHANMPIKIEAVSLPKFLEWLNEQ
Sequence of entity 3 (c), FASTA
>8DH6_3 Cytochrome c oxidase subunit 3 (chains c)
MTHLERSRHQQHPFHMVMPSPWPIVVSFALLSLALSTALTMHGYIGNMNMVYLALFVLLT
SSILWFRDIVAEATYLGDHTMAVRKGINLGFLMFVLSEVLIFAGLFWAYFHSAMSPDVTL
GACWPPVGIEAVQPTELPLLNTIILLSSGATVTYSHHALIAGNRNKALSGLLITFWLIVI
FVTCQYIEYTNAAFTISDGVYGSVFYAGTGLHFLHMVMLAAMLGVNYWRMRNYHLTAGHH
VGYETTIIYTHVLDVIWLFLYVVFYWWGV
Sequence of entity 4 (d), FASTA
>8DH6_4 Cytochrome c oxidase subunit 4, mitochondrial (chains d)
QQKPVVKTAQNLAEVNGPETLIGPGAKEGTVPTDLDQETGLARLELLGKLEGIDVFDTKP
LDSSRKGTMKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNP
VGVPNDDHHH
Sequence of entity 5 (e), FASTA
>8DH6_5 Cytochrome c oxidase subunit 5A, mitochondrial (chains e)
AQTHALSNAAVMDLQSRWENMPSTEQQDIVSKLSERQKLPWAQLTEPEKQAVWYISYGEW
GPRRPVLNKGDSSFIAKGVAAGLLFSVGLFAVVRMAGGQDAKTMNKEWQLKSDEYLKSKN
ANPWGGYSQVQSK
Sequence of entity 6 (f), FASTA
>8DH6_6 Cytochrome c oxidase subunit 6, mitochondrial (chains f)
SDAHDEETFEEFTARYEKEFDEAYDLFEVQRVLNNCFSYDLVPAPAVIEKALRAARRVND
LPTAIRVFEALKYKVENEDQYKAYLDELKDVRQELGVPLKEELFPSSS
Sequence of entity 7 (g), FASTA
>8DH6_7 Cytochrome c oxidase subunit 7, mitochondrial (chains g)
ANKVIQLQKIFQSSTKPLWWRHPRSALYLYPFYAIFAVAVVTPLLYIPNAIRGIKAKKA
Sequence of entity 8 (h), FASTA
>8DH6_8 Cytochrome c oxidase subunit 8, mitochondrial (chains h)
VHFKDGVYENIPFKVKGRKTPYALSHFGFFAIGFAVPFVACYVQLKKSGAF
Sequence of entity 9 (i), FASTA
>8DH6_9 Cytochrome c oxidase subunit 9, mitochondrial (chains i)
TIAPITGTIKRRVIMDIVLGFSLGGVMASYWWWGFHMDKINKREKFYAELAERKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CU | Copper (II) ion | Cu | 2 |
| ZN | Zinc ion | Zn | 1 |
| PEF | Di-palmitoyl-3-sn-phosphatidylethanolamine | C37 H74 N O8 P | 10 |
| HEA | Heme-a | C49 H56 Fe N4 O6 | 2 |
| MG | Magnesium ion | Mg | 1 |
| CA | Calcium ion | Ca | 1 |
Primary citation
Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs. Godoy, A.S., Song, Y., Cheruvara, H. et al. To be published.
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
- 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
- 7Z10 3.87 Å, Monomeric respiratory complex IV isolated from S. cerevisiae
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