6YMX: Cytochrome c oxidase subunit 1

CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae. Determined by electron microscopy at 3.17 Å resolution. Released 9 Sept 2020.

Method
Electron microscopy
Resolution
3.17 Å
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains
32
Atoms
47,034
Mol. weight
669.79 kDa
Ligands
FES, 7PH, 9PE, UQ6
Released
9 Sept 2020

Explore 6YMX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YMX contains 329 α-helices and 142 β-strands across 32 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: 37 helices, 2 β-strands

ElementResiduesLengthSheet
α-helix11-2111
α-helix26-294
α-helix31-399
α-helix58-669
α-helix67-715
α-helix721
α-helix73-786
α-helix80-834
α-helix98-1047
α-helix108-11811
α-helix143-1475
α-helix150-16314
α-helix166-1694
α-helix184-19613
α-helix200-21516
α-helix232-24413
α-helix251-2588
α-helix266-2672
α-helix270-28314
α-helix293-2953
α-helix301-3088
α-helix311-3133
α-helix315-3217
α-helix336-35823
α-helix364-3663
β-strand37011
α-helix371-3777
α-helix390-40011
α-helix407-4104
α-helix412-42514
α-helix428-4347
α-helix4361
β-strand43711
α-helix445-4484
α-helix450-4567
α-helix458-47619
α-helix501-5044
α-helix514-5163
α-helix522-5232
Chain A: 21 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand29-33510
β-strand37-42610
β-strand49-55710
α-helix69-779
α-helix80-889
β-strand92-97610
β-strand102-108710
α-helix115-1206
α-helix121-1266
α-helix134-15219
α-helix156-16813
α-helix173-1753
α-helix182-1854
α-helix190-20011
β-strand206-212710
α-helix216-2249
α-helix235-2384
β-strand247-253711
β-strand259-266811
α-helix268-2692
α-helix275-28511
β-strand287-289311
α-helix303-3064
β-strand314-321811
β-strand326-333811
α-helix340-35617
α-helix360-37314
α-helix383-39412
α-helix400-4023
α-helix403-4064
α-helix415-42511
β-strand432-437611
α-helix446-4494
Chain b: 12 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix25-284
α-helix31-4515
α-helix48-5710
α-helix59-624
α-helix79-824
α-helix84-874
α-helix89-968
α-helix98-1047
β-strand115-12172
β-strand126-12942
β-strand142-14432
α-helix1461
β-strand14713
α-helix148-1492
α-helix157-1582
β-strand16313
β-strand168-16924
β-strand175-18172
β-strand188-19035
β-strand195-19735
β-strand20512
β-strand215-21734
β-strand22015
β-strand236-23834
α-helix241-2488
Chain B: 19 helices, 17 β-strands
ElementResiduesLengthSheet
β-strand18-22512
β-strand28-36912
α-helix39-413
α-helix47-548
β-strand59113
α-helix65-717
β-strand76-82712
β-strand86-94912
α-helix98-11114
β-strand112113
α-helix116-1183
α-helix119-1235
α-helix124-13411
α-helix138-14710
α-helix169-17911
β-strand185-190612
α-helix194-2018
α-helix205-2073
α-helix220-2223
β-strand228-232514
β-strand238114
β-strand241-245514
α-helix250-25910
β-strand273115
β-strand276-278314
β-strand283-287514
β-strand288115
α-helix301-3088
β-strand312-313216
α-helix316-3183
α-helix320-3289
α-helix340-3423
β-strand345-346216
β-strand352-357614
α-helix363-3642
α-helix365-3673
Chain c: 15 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix6-83
α-helix22-3716
α-helix50-7324
α-helix81-9010
α-helix103-1097
α-helix131-1333
α-helix137-14610
α-helix156-1616
β-strand16316
α-helix164-1674
α-helix169-18416
α-helix199-20810
α-helix216-23116
α-helix244-2518
α-helix253-2619
α-helix262-2665
Chain C: 26 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix3-64
α-helix10-134
α-helix14-185
β-strand22-23217
α-helix28-314
α-helix32-4817
α-helix66-716
α-helix75-9420
α-helix99-1024
α-helix111-13222
β-strand137118
α-helix138-14710
α-helix150-1534
α-helix158-1669
α-helix173-19321
α-helix195-2028
β-strand218-219217
α-helix226-24520
α-helix254-2574
β-strand259118
α-helix2601
α-helix276-2827
α-helix289-30012
α-helix305-3084
β-strand313119
α-helix321-33919
α-helix350-3545
α-helix357-3615
α-helix362-3665
α-helix367-3704
α-helix373-3808
Chain d: 4 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix43-453
α-helix49-524
β-strand5516
α-helix66-749
α-helix971
β-strand98-9927
β-strand10918
β-strand12418
β-strand13217
β-strand141-14227
Chain D: 16 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix64-674
α-helix69-724
α-helix88-969
α-helix97-1015
β-strand111120
α-helix112-1143
β-strand116121
β-strand120121
α-helix122-1287
β-strand133-135322
β-strand146-148322
β-strand154120
α-helix155-1573
α-helix162-1687
α-helix172-1765
α-helix188-1958
α-helix208-2092
β-strand213-214223
β-strand222-223223
α-helix244-25916
α-helix263-27614
α-helix280-29112
α-helix293-2964
β-strand299-302411
α-helix304-3063

24 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cytochrome c oxidase subunit 1aprotein530Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P00401 (AlphaFold model)
Cytochrome c oxidase subunit 2bprotein236Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P00410 (AlphaFold model)
Cytochrome c oxidase subunit 3cprotein268Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P00420 (AlphaFold model)
Cytochrome c oxidase subunit 4, mitochondrialdprotein117Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P04037 (AlphaFold model)
Cytochrome c oxidase subunit 5A, mitochondrialeprotein128Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P00424
Cytochrome c oxidase subunit 6, mitochondrialfprotein99Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P00427
Cytochrome c oxidase subunit 7, mitochondrialgprotein55Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P10174
Cytochrome c oxidase subunit 8, mitochondrialhprotein51Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P04039
Cytochrome c oxidase subunit 9, mitochondrialiprotein53Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P07255
Cytochrome c oxidase subunit 12, mitochondrialjprotein78Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Q01519
Cytochrome c oxidase subunit 13, mitochondrialkprotein114Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P32799
Cytochrome c oxidase subunit 26, mitochondrialmprotein38Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Q2V2P9

13 more molecules are not listed.

Sequence of entity 1 (a), FASTA
>6YMX_1 Cytochrome c oxidase subunit 1 (chains a)
WLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVVGHAV
LMIFFLVMPALIGGFGNYLLPLMIGATDTAFPRINNIAFWVLPMGLVCLVTSTLVESGAG
TGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMHKLPL
FVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFGHPEV
YILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDADTRAY
FTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALANASLD
VAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIGANVI
FFPMHFLGINGMPRRIPDYPDAFAGWNYVASIGSFIATLSLFLFIYILYDQLVNGLNNKV
NNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS
Sequence of entity 2 (b), FASTA
>6YMX_2 Cytochrome c oxidase subunit 2 (chains b)
DVPTPYACYFQDSATPNQEGILELHDNIMFYLLVILGLVSWMLYTIVMTYSKNPIAYKYI
KHGQTIEVIWTIFPAVILLIIAFPSFILLYLCDEVISPAMTIKAIGYQWYWKYEYSDFIN
DSGETVEFESYVIPDELLEEGQLRLLDTDTSMVVPVDTHIRFVVTAADVIHDFAIPSLGI
KVDATPGRLNQVSALIQREGVFYGACSELCGTGHANMPIKIEAVSLPKFLEWLNEQ
Sequence of entity 3 (c), FASTA
>6YMX_3 Cytochrome c oxidase subunit 3 (chains c)
THLERSRHQQHPFHMVMPSPWPIVVSFALLSLALSTALTMHGYIGNMNMVYLALFVLLTS
SILWFRDIVAEATYLGDHTMAVRKGINLGFLMFVLSEVLIFAGLFWAYFHSAMSPDVTLG
ACWPPVGIEAVQPTELPLLNTIILLSSGATVTYSHHALIAGNRNKALSGLLITFWLIVIF
VTCQYIEYTNAAFTISDGVYGSVFYAGTGLHFLHMVMLAAMLGVNYWRMRNYHLTAGHHV
GYETTIIYTHVLDVIWLFLYVVFYWWGV
Sequence of entity 4 (d), FASTA
>6YMX_4 Cytochrome c oxidase subunit 4, mitochondrial (chains d)
VVKTAQNLAEVNGPETLIGPGAKEGTVPTDLDQETGLARLELLGKLEGIDVFDTKPLDSS
RKGTMKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNPV
Sequence of entity 5 (e), FASTA
>6YMX_5 Cytochrome c oxidase subunit 5A, mitochondrial (chains e)
ALSNAAVMDLQSRWENMPSTEQQDIVSKLSERQKLPWAQLTEPEKQAVWYISYGEWGPRR
PVLNKGDSSFIAKGVAAGLLFSVGLFAVVRMAGGQDAKTMNKEWQLKSDEYLKSKNANPW
GGYSQVQS
Sequence of entity 6 (f), FASTA
>6YMX_6 Cytochrome c oxidase subunit 6, mitochondrial (chains f)
ETFEEFTARYEKEFDEAYDLFEVQRVLNNCFSYDLVPAPAVIEKALRAARRVNDLPTAIR
VFEALKYKVENEDQYKAYLDELKDVRQELGVPLKEELFP
Sequence of entity 7 (g), FASTA
>6YMX_7 Cytochrome c oxidase subunit 7, mitochondrial (chains g)
NKVIQLQKIFQSSTKPLWWRHPRSALYLYPFYAIFAVAVVTPLLYIPNAIRGIKA
Sequence of entity 8 (h), FASTA
>6YMX_8 Cytochrome c oxidase subunit 8, mitochondrial (chains h)
VHFKDGVYENIPFKVKGRKTPYALSHFGFFAIGFAVPFVACYVQLKKSGAF
Sequence of entity 9 (i), FASTA
>6YMX_9 Cytochrome c oxidase subunit 9, mitochondrial (chains i)
IAPITGTIKRRVIMDIVLGFSLGGVMASYWWWGFHMDKINKREKFYAELAERK
Sequence of entity 10 (j), FASTA
>6YMX_10 Cytochrome c oxidase subunit 12, mitochondrial (chains j)
NSPLHTVGFDARFPQQNQTKHCWQSYVDYHKCVNMKGEDFAPCKVFWKTYNALCPLDWIE
KWDDQREKGIFAGDINSD
Sequence of entity 11 (k), FASTA
>6YMX_11 Cytochrome c oxidase subunit 13, mitochondrial (chains k)
NALKPAFGPPDKVAAQKFKESLMATEKHAKDTSNMWVKISVWVALPAIALTAVNTYFVEK
EHAEHREHLKHVPDSEWPRDYEFMNIRSKPFFWGDGDKTLFWNPVVNRHIEHDD
Sequence of entity 12 (m), FASTA
>6YMX_12 Cytochrome c oxidase subunit 26, mitochondrial (chains m)
ESWVITEGRRLIPEIFQWSAVLSVCLGWPGAVYFFSKA

Ligands and cofactors

IDNameFormulaCopies
FESFE2/S2 (inorganic) clusterFe2 S22
7PH(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoateC29 H57 O8 P2
9PE(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]et…C30 H60 N O8 P2
UQ65-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy…C39 H60 O42
CN5(5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-dipho…C26 H52 O13 P21
8PE(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl…C37 H74 N O8 P2
HEMProtoporphyrin IX containing FEC34 H32 Fe N4 O46
6PH(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoateC31 H61 O8 P2
ZNZinc ionZn1
PCF1,2-diacyl-sn-glycero-3-phoshocholineC40 H80 N O8 P5
CUADinuclear copper ionCu21
CN3(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(prop…C36 H68 O17 P22
PTYPhosphatidylethanolamineC40 H80 N O8 P7
HEAHeme-aC49 H56 Fe N4 O62
CUCopper (II) ionCu1

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:

Browse structure collections

About this viewer

MolViewer shows 6YMX directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.