9BPB: Cytochrome b-c1 complex subunit 1, mitochondrial

Tethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae. Determined by electron microscopy at 2.57 Å resolution. Released 21 May 2025.

Method
Electron microscopy
Resolution
2.57 Å
Organism
Saccharomyces cerevisiae W303
Chains
42
Atoms
60,828
Mol. weight
990.98 kDa
Ligands
ZN, CUA, MG, CN3
Released
21 May 2025

Explore 9BPB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BPB contains 392 α-helices and 174 β-strands across 42 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.

Chains a and m: 27 helices, 5 β-strands

ElementResiduesLengthSheet
α-helix2-65
α-helix11-3929
α-helix56-6611
α-helix67-8014
α-helix81-888
α-helix98-11821
α-helix143-17129
α-helix184-21532
α-helix231-24616
α-helix249-25810
β-strand263131
α-helix270-28314
α-helix284-2863
α-helix289-2924
α-helix299-31012
α-helix313-32513
β-strand332131
α-helix336-35823
α-helix364-3663
β-strand370132
α-helix371-38010
α-helix385-40016
α-helix407-42519
α-helix428-4336
α-helix4361
β-strand437132
α-helix445-4473
α-helix448-47629
α-helix514-5174
α-helix522-5232
α-helix530-5312
β-strand532-533233
Chains A and K: 26 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand29-3241
β-strand37-4261
β-strand49-5571
α-helix59-613
α-helix69-779
α-helix80-8910
β-strand92-9761
β-strand102-10871
α-helix110-1123
α-helix113-1197
α-helix120-1267
α-helix134-15421
α-helix156-16813
α-helix173-1753
α-helix182-1876
α-helix190-20011
α-helix203-2053
β-strand206-21271
α-helix216-22510
α-helix235-2384
β-strand247-25372
β-strand259-26682
α-helix268-2692
α-helix275-28511
β-strand288-28922
α-helix294-2963
α-helix303-3064
β-strand314-32182
β-strand326-33492
α-helix340-35718
α-helix360-37819
α-helix383-39412
α-helix403-4119
α-helix415-42511
β-strand432-43762
α-helix439-4413
α-helix445-4495
α-helix450-4523
Chains b and n: 8 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix25-284
α-helix31-6535
α-helix79-10628
β-strand115-121734
β-strand126-130534
β-strand141-145534
α-helix1461
β-strand147135
α-helix148-1492
α-helix157-1582
β-strand163135
β-strand167-170436
β-strand174-181834
β-strand188-190337
α-helix191-1933
β-strand195-197337
β-strand205-210634
β-strand215-217336
β-strand220-221237
β-strand236-239436
α-helix241-2488
Chains B and L: 19 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand18-2253
β-strand28-3583
α-helix39-413
α-helix47-548
β-strand5914
α-helix64-7310
β-strand77-8263
β-strand87-9483
α-helix98-10811
β-strand11214
α-helix116-1183
α-helix119-1235
α-helix124-13613
α-helix138-15013
α-helix169-17911
β-strand185-19063
α-helix194-2018
α-helix205-2084
α-helix220-2223
β-strand228-23255
β-strand237-24595
α-helix250-25910
α-helix266-2694
β-strand273-27865
β-strand283-28865
β-strand290-29125
α-helix294-31017
β-strand312-31326
α-helix315-3173
α-helix318-32811
α-helix338-3425
β-strand345-34626
β-strand352-35765
α-helix363-3642
Chains c and o: 12 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix3-64
α-helix17-193
α-helix22-4019
α-helix49-7426
α-helix81-11434
α-helix1261
α-helix131-1333
α-helix138-16124
α-helix164-19027
α-helix199-23133
α-helix241-26121
α-helix262-2665
Chains C and M: 24 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix3-64
α-helix10-134
α-helix14-185
β-strand21-2337
α-helix28-314
α-helix32-4817
α-helix51-533
α-helix61-7010
α-helix75-10228
α-helix111-13424
β-strand13718
α-helix138-14811
α-helix149-1535
α-helix158-1669
α-helix173-20129
β-strand218-22037
α-helix225-24521
α-helix254-2574
β-strand25918
α-helix2601
α-helix276-2849
α-helix289-30012
α-helix301-3044
α-helix305-3084
β-strand31319
α-helix322-33918
α-helix348-36114
α-helix362-3665
α-helix367-38014
Chains d and p: 5 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix43-464
α-helix49-524
α-helix66-7510
α-helix84-874
β-strand93138
β-strand96138
α-helix971
β-strand98-102539
β-strand106140
β-strand109-111333
β-strand122-124333
β-strand127140
β-strand130140
β-strand131-132239
β-strand141-145539
Chains D and N: 16 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix69-713
α-helix87-9610
α-helix97-1015
β-strand106110
β-strand111111
α-helix113-1153
β-strand116112
β-strand120112
α-helix122-1287
β-strand133-136413
α-helix137-1382
β-strand145-148413
β-strand154111
α-helix155-1573
α-helix162-1687
α-helix174-1752
β-strand176110
α-helix187-1959
α-helix202-2032
α-helix208-2092
β-strand213-214214
β-strand222-223214
α-helix244-25916
α-helix263-29129
α-helix293-2964
β-strand299-30242
α-helix304-3063

13 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 b-c1 complex subunit 1, mitochondrialA, Kprotein457Saccharomyces cerevisiae W303P07256 (AlphaFold model)
Cytochrome b-c1 complex subunit 2, mitochondrialB, Lprotein368Saccharomyces cerevisiae W303P07257 (AlphaFold model)
Cytochrome bC, Mprotein385Saccharomyces cerevisiae W303P00163 (AlphaFold model)
Cytochrome c1, heme protein, mitochondrialD, Nprotein309Saccharomyces cerevisiae W303P07143 (AlphaFold model)
Cytochrome b-c1 complex subunit Rieske, mitochondrialE, Oprotein215Saccharomyces cerevisiae W303P08067
Cytochrome b-c1 complex subunit 6, mitochondrialF, Pprotein147Saccharomyces cerevisiae W303P00127
Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrialG, Qprotein183Saccharomyces cerevisiae W303P00128, P04039
Cytochrome b-c1 complex subunit 8, mitochondrialH, Rprotein94Saccharomyces cerevisiae W303P08525
Cytochrome b-c1 complex subunit 9, mitochondrialI, Sprotein66Saccharomyces cerevisiae W303P22289
Cytochrome b-c1 complex subunit 10, mitochondrialJ, Tprotein77Saccharomyces cerevisiae W303P37299
Cytochrome c oxidase subunit 1a, mprotein534Saccharomyces cerevisiae W303P00401
Cytochrome c oxidase subunit 2b, nprotein251Saccharomyces cerevisiae W303P00410

9 more molecules are not listed.

Sequence of entity 1 (A, K), FASTA
>9BPB_1 Cytochrome b-c1 complex subunit 1, mitochondrial (chains A, K)
MLRTVTSKTVSNQFKRSLATAVATPKAEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAA
NENPYNNGVSNLWKNIFLSKENSAVAAKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFL
NQSFIQQKANLLSSSNFEATKKSVLKQVQDFEENDHPNRVLEHLHSTAFQNTPLSLPTRG
TLESLENLVVADLESFANNHFLNSNAVVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKK
KAAFLGSEVRLRDDTLPKAWISLAVEGEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGI
KLLDNIQEYQLCDNFNHFSLSYKDSGLWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTD
TEVERAKSLLKLQLGQLYESGNPVNDANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKA
WAGKRLWDQDIAIAGTGQIEGLLDYMRIRSDMSMMRW
Sequence of entity 2 (B, L), FASTA
>9BPB_2 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B, L)
MLSAARLQFAQGSVRRLTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTN
TRSALKLVRESELLGGTFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELT
ESVLPAARYDYAVAEQCPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVY
TKENLEVSGENVVEADLKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAA
IGIPVNKASLAQYEVLANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSN
IKKIVADLKKGKDLSPAINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVS
NLPYLDEL
Sequence of entity 3 (C, M), FASTA
>9BPB_3 Cytochrome b (chains C, M)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK
Sequence of entity 4 (D, N), FASTA
>9BPB_4 Cytochrome c1, heme protein, mitochondrial (chains D, N)
MFSNLSKRWAQRTLSKSFYSTATGAASKSGKLTQKLVTAGVAAAGITASTLLYADSLTAE
AMTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSH
TNEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLI
VKARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGT
PATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKF
VFNPPKPRK
Sequence of entity 5 (E, O), FASTA
>9BPB_5 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains E, O)
MLGIRSSVKTCFKPMSLTSKRLISQSLLASKSTYRTPNFDDVLKENNDADKGRSYAYFMV
GAMGLLSSAGAKSTVETFISSMTATADVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRH
RTPHEIQEANSVDMSALKDPQTDADRVKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPC
HGSHYDISGRIRKGPAPLNLEIPAYEFDGDKVIVG
Sequence of entity 6 (F, P), FASTA
>9BPB_6 Cytochrome b-c1 complex subunit 6, mitochondrial (chains F, P)
MGMLELVGEYWEQLKITVVPVVAAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDD
DDDDDEDEEEEEEVTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHK
EDCVEEFFHLQHYLDTATAPRLFDKLK
Sequence of entity 7 (G, Q), FASTA
>9BPB_7 Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrial (chains G, Q)
MPQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTAL
RRLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDEL
DNIEVSKGGGGSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIGFAVPFVACYVQLKKS
GAF
Sequence of entity 8 (H, R), FASTA
>9BPB_8 Cytochrome b-c1 complex subunit 8, mitochondrial (chains H, R)
MGPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVL
IPAGIYWYWWKNGNEYNEFLYSKAGREELERVNV
Sequence of entity 9 (I, S), FASTA
>9BPB_9 Cytochrome b-c1 complex subunit 9, mitochondrial (chains I, S)
MSFSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAAGD
GDDDDE
Sequence of entity 10 (J, T), FASTA
>9BPB_10 Cytochrome b-c1 complex subunit 10, mitochondrial (chains J, T)
MAYTSHLSSKTGLHFGRLSLRSLTAYAPNLMLWGGASMLGLFVFTEGWPKFQDTLYKKIP
LLGPTLEDHTPPEDKPN
Sequence of entity 11 (a, m), FASTA
>9BPB_11 Cytochrome c oxidase subunit 1 (chains a, m)
MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVV
GHAVLMIFFLVMPALIGGFGNYLLPLMIGATDTAFPRINNIAFWVLPMGLVCLVTSTLVE
SGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMH
KLPLFVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFG
HPEVYILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDAD
TRAYFTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALAN
ASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIG
ANVIFFPMHFLGINGMPRRIPDYPDAFAGWNYVASIGSFIATLSLFLFIYILYDQLVNGL
NNKVNNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS
Sequence of entity 12 (b, n), FASTA
>9BPB_12 Cytochrome c oxidase subunit 2 (chains b, n)
MLDLLRLQLTTFIMNDVPTPYACYFQDSATPNQEGILELHDNIMFYLLVILGLVSWMLYT
IVMTYSKNPIAYKYIKHGQTIEVIWTIFPAVILLIIAFPSFILLYLCDEVISPAMTIKAI
GYQWYWKYEYSDFINDSGETVEFESYVIPDELLEEGQLRLLDTDTSMVVPVDTHIRFVVT
AADVIHDFAIPSLGIKVDATPGRLNQVSALIQREGVFYGACSELCGTGHANMPIKIEAVS
LPKFLEWLNEQ

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn2
CUADinuclear copper ionCu22
MGMagnesium ionMg2
CN3(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(prop…C36 H68 O17 P22
CACalcium ionCa2
CUCopper (II) ionCu2
HEAHeme-aC49 H56 Fe N4 O64
PTYPhosphatidylethanolamineC40 H80 N O8 P10
PCF1,2-diacyl-sn-glycero-3-phoshocholineC40 H80 N O8 P8
FESFE2/S2 (inorganic) clusterFe2 S22
HECHeme CC34 H36 Fe N4 O42
PEFDi-palmitoyl-3-sn-phosphatidylethanolamineC37 H74 N O8 P6
9PE(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]et…C30 H60 N O8 P2
HEMProtoporphyrin IX containing FEC34 H32 Fe N4 O44
UQ65-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy…C39 H60 O44
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
6PH(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoateC31 H61 O8 P2
CDLCardiolipinC81 H156 O17 P28

Primary citation

Mitochondrial respirasome-like supercomplexes support metabolic flexibility in yeast. Eldeeb, M.H., Cosner, Z., Carlstrom, A. et al. Nat Commun (2026). DOI 10.1038/s41467-026-72228-8 · PubMed

Other PDB entries of the same protein (UniProt P07256 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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