8EC0: Cytochrome b-c1 complex subunit 1, mitochondrial

III2IV respiratory supercomplex from Saccharomyces cerevisiae cardiolipin-lacking mutant. Determined by electron microscopy at 3.3 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Saccharomyces cerevisiae
Chains: 30
Atoms: 46,624
Mol. weight: 735.12 kDa
Ligands: PEF, PGT, FES, PCF
Released: 24 May 2023

Explore 8EC0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EC0 contains 259 α-helices and 121 β-strands across 30 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: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	30-34	5	27
β-strand	36-40	5	27
β-strand	42	1	28
β-strand	50-55	6	27
α-helix	70-77	8
α-helix	81-88	8
β-strand	93-96	4	27
β-strand	102-107	6	27
α-helix	113-124	12
α-helix	134-153	20
α-helix	156-168	13
α-helix	182-187	6
α-helix	191-200	10
β-strand	206-209	4	27
β-strand	212	1	28
α-helix	217-221	5
α-helix	235-238	4
β-strand	248-251	4	29
β-strand	252-253	2	7
β-strand	259-266	8	29
α-helix	275-285	11
β-strand	288-289	2	29
α-helix	301-308	8
β-strand	314-316	3	29
β-strand	319-321	3	29
β-strand	326-334	9	29
α-helix	337-339	3
α-helix	340-356	17
α-helix	360-378	19
α-helix	383-397	15
α-helix	400-402	3
α-helix	403-411	9
α-helix	415-425	11
β-strand	431	1	29
β-strand	433-437	5	29
α-helix	446-449	4

Chain A: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	28-34	7	1
β-strand	36-42	7	1
β-strand	50-55	6	1
α-helix	69-79	11
α-helix	82-88	7
β-strand	93	1	1
β-strand	96	1	1
β-strand	102-107	6	1
α-helix	113-124	12
α-helix	134-153	20
α-helix	156-168	13
α-helix	182-185	4
α-helix	191-200	10
β-strand	206-209	4	1
β-strand	212	1	1
α-helix	217-221	5
α-helix	235-237	3
β-strand	247-252	6	2
β-strand	259-266	8	2
α-helix	275-285	11
β-strand	288-289	2	2
α-helix	301-307	7
β-strand	314-315	2	2
β-strand	319-321	3	2
β-strand	326-334	9	2
α-helix	340-354	15
α-helix	360-379	20
α-helix	383-394	12
α-helix	403-412	10
α-helix	415-425	11
β-strand	432-437	6	2
α-helix	446-450	5

Chain b: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	30
β-strand	29-35	7	30
α-helix	47-53	7
α-helix	66-72	7
β-strand	76-82	7	30
β-strand	87-93	7	30
α-helix	98-108	11
α-helix	116-118	3
α-helix	124-136	13
α-helix	138-150	13
α-helix	169-179	11
β-strand	186-190	5	30
α-helix	194-200	7
α-helix	205-208	4
α-helix	220-222	3
β-strand	228-231	4	31
β-strand	237-241	5	31
β-strand	243-245	3	32
α-helix	251-261	11
β-strand	273	1	31
β-strand	276-278	3	32
β-strand	283-285	3	32
β-strand	288-291	4	31
α-helix	295-310	16
α-helix	315-317	3
α-helix	318-328	11
β-strand	353-356	4	31

Chain B: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	3
β-strand	22	1	4
β-strand	28-35	8	3
α-helix	47-53	7
α-helix	69-74	6
β-strand	77-80	4	3
β-strand	87-94	8	3
α-helix	98-108	11
α-helix	116-118	3
α-helix	119-123	5
α-helix	124-136	13
α-helix	138-150	13
α-helix	169-179	11
β-strand	186-188	3	3
β-strand	190	1	4
α-helix	194-199	6
α-helix	205-208	4
β-strand	228-232	5	5
β-strand	237-242	6	5
β-strand	243-245	3	6
α-helix	251-261	11
β-strand	276-278	3	6
β-strand	283-285	3	6
β-strand	290-291	2	5
α-helix	294-308	15
α-helix	318-328	11
β-strand	352-357	6	5

Chain c: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
α-helix	49-82	34
α-helix	91-92	2
β-strand	95-97	3	33
β-strand	106-111	6	34
β-strand	114-120	7	34
α-helix	123-130	8
α-helix	143-146	4
β-strand	152-156	5	34
α-helix	164-166	3
β-strand	167-168	2	35
β-strand	176-177	2	35
β-strand	184-185	2	35
α-helix	199-201	3
β-strand	206-207	2	33
β-strand	211-213	3	33

Chain C: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
α-helix	50-83	34
α-helix	87-89	3
β-strand	94-97	4	8
β-strand	106-111	6	9
β-strand	114-120	7	9
α-helix	123-130	8
α-helix	134-136	3
α-helix	143-146	4
β-strand	152-156	5	9
α-helix	164-166	3
β-strand	167-168	2	10
β-strand	176-177	2	10
β-strand	185	1	10
α-helix	199-201	3
β-strand	205-208	4	8
β-strand	211-214	4	8

Chain e: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	5-7	3
α-helix	9-11	3
α-helix	15-43	29
α-helix	49-54	6

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	5-9	5
α-helix	17-42	26
α-helix	52-56	5

22 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 b-c1 complex subunit 1, mitochondrial	A, a	protein	457	Saccharomyces cerevisiae	P07256 (AlphaFold model)
Cytochrome b-c1 complex subunit 2, mitochondrial	B, b	protein	368	Saccharomyces cerevisiae	P07257 (AlphaFold model)
Cytochrome b-c1 complex subunit Rieske, mitochondrial	C, c	protein	215	Saccharomyces cerevisiae	P08067 (AlphaFold model)
Cytochrome b-c1 complex subunit 9, mitochondrial	E, e	protein	66	Saccharomyces cerevisiae	P22289 (AlphaFold model)
Cytochrome b-c1 complex subunit 7, mitochondrial	F, f	protein	127	Saccharomyces cerevisiae	P00128
Cytochrome b-c1 complex subunit 6, mitochondrial	G, g	protein	147	Saccharomyces cerevisiae	P00127
Cytochrome b-c1 complex subunit 8, mitochondrial	H, h	protein	94	Saccharomyces cerevisiae	P08525
Cytochrome b	J, j	protein	385	Saccharomyces cerevisiae	P00163
Cytochrome c oxidase subunit 1	K	protein	534	Saccharomyces cerevisiae	P00401
Cytochrome c1, heme protein, mitochondrial	L, l	protein	309	Saccharomyces cerevisiae	P07143
Cytochrome c oxidase subunit 8, mitochondrial	M	protein	78	Saccharomyces cerevisiae	P04039
Cytochrome c oxidase subunit 7, mitochondrial	N	protein	60	Saccharomyces cerevisiae	P10174

9 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA

>8EC0_1 Cytochrome b-c1 complex subunit 1, mitochondrial (chains A, a)
MLRTVTSKTVSNQFKRSLATAVATPKAEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAA
NENPYNNGVSNLWKNIFLSKENSAVAAKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFL
NQSFIQQKANLLSSSNFEATKKSVLKQVQDFEENDHPNRVLEHLHSTAFQNTPLSLPTRG
TLESLENLVVADLESFANNHFLNSNAVVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKK
KAAFLGSEVRLRDDTLPKAWISLAVEGEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGI
KLLDNIQEYQLCDNFNHFSLSYKDSGLWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTD
TEVERAKSLLKLQLGQLYESGNPVNDANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKA
WAGKRLWDQDIAIAGTGQIEGLLDYMRIRSDMSMMRW

Sequence of entity 2 (B, b), FASTA

>8EC0_2 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B, b)
MLSAARLQFAQGSVRRLTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTN
TRSALKLVRESELLGGTFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELT
ESVLPAARYDYAVAEQCPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVY
TKENLEVSGENVVEADLKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAA
IGIPVNKASLAQYEVLANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSN
IKKIVADLKKGKDLSPAINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVS
NLPYLDEL

Sequence of entity 3 (C, c), FASTA

>8EC0_3 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains C, c)
MLGIRSSVKTCFKPMSLTSKRLISQSLLASKSTYRTPNFDDVLKENNDADKGRSYAYFMV
GAMGLLSSAGAKSTVETFISSMTATADVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRH
RTPHEIQEANSVDMSALKDPQTDADRVKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPC
HGSHYDISGRIRKGPAPLNLEIPAYEFDGDKVIVG

Sequence of entity 4 (E, e), FASTA

>8EC0_4 Cytochrome b-c1 complex subunit 9, mitochondrial (chains E, e)
MSFSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAAGD
GDDDDE

Sequence of entity 5 (F, f), FASTA

>8EC0_5 Cytochrome b-c1 complex subunit 7, mitochondrial (chains F, f)
MPQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTAL
RRLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDEL
DNIEVSK

Sequence of entity 6 (G, g), FASTA

>8EC0_6 Cytochrome b-c1 complex subunit 6, mitochondrial (chains G, g)
MGMLELVGEYWEQLKITVVPVVAAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDD
DDDDDEDEEEEEEVTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHK
EDCVEEFFHLQHYLDTATAPRLFDKLK

Sequence of entity 7 (H, h), FASTA

>8EC0_7 Cytochrome b-c1 complex subunit 8, mitochondrial (chains H, h)
MGPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVL
IPAGIYWYWWKNGNEYNEFLYSKAGREELERVNV

Sequence of entity 8 (J, j), FASTA

>8EC0_8 Cytochrome b (chains J, j)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK

Sequence of entity 9 (K), FASTA

>8EC0_9 Cytochrome c oxidase subunit 1 (chains K)
MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVV
GHAVLMIFFLVMPALIGGFGNYLLPLMIGATDTAFPRINNIAFWVLPMGLVCLVTSTLVE
SGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMH
KLPLFVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFG
HPEVYILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDAD
TRAYFTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALAN
ASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIG
ANVIFFPMHFLGINGMPRRIPDYPDAFAGWNYVASIGSFIATLSLFLFIYILYDQLVNGL
NNKVNNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS

Sequence of entity 10 (L, l), FASTA

>8EC0_10 Cytochrome c1, heme protein, mitochondrial (chains L, l)
MFSNLSKRWAQRTLSKSFYSTATGAASKSGKLTQKLVTAGVAAAGITASTLLYADSLTAE
AMTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSH
TNEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLI
VKARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGT
PATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKF
VFNPPKPRK

Sequence of entity 11 (M), FASTA

>8EC0_11 Cytochrome c oxidase subunit 8, mitochondrial (chains M)
MLCQQMIRTTAKRSSNIMTRPIIMKRSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIG
FAVPFVACYVQLKKSGAF

Sequence of entity 12 (N), FASTA

>8EC0_12 Cytochrome c oxidase subunit 7, mitochondrial (chains N)
MANKVIQLQKIFQSSTKPLWWRHPRSALYLYPFYAIFAVAVVTPLLYIPNAIRGIKAKKA

Ligands and cofactors

ID	Name	Formula	Copies
PEF	Di-palmitoyl-3-sn-phosphatidylethanolamine	C37 H74 N O8 P	15
PGT	(1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoylo…	C40 H79 O10 P	7
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
PCF	1,2-diacyl-sn-glycero-3-phoshocholine	C40 H80 N O8 P	4
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	6
UQ6	5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy…	C39 H60 O4	2
CU	Copper (II) ion	Cu	1
HEA	Heme-a	C49 H56 Fe N4 O6	2
CUA	Dinuclear copper ion	Cu2	2

Primary citation

Structural insights into cardiolipin replacement by phosphatidylglycerol in a cardiolipin-lacking yeast respiratory supercomplex. Hryc, C.F., Mallampalli, V.K.P.S., Bovshik, E.I. et al. Nat Commun (2023) 14:2783-2783. DOI 10.1038/s41467-023-38441-5 · PubMed

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

3CX5 1.9 Å, Structure of complex III with bound cytochrome c in reduced state and definition of a…
1EZV 2.3 Å, Structure of the yeast cytochrome BC1 complex co-crystallized with an antibody fv-fragment
1KB9 2.3 Å, Yeast cytochrome BC1 complex
2IBZ 2.3 Å, Yeast Cytochrome BC1 Complex with Stigmatellin
8YIO 2.35 Å, Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in azoxystrobin-bound state
9ETZ 2.4 Å, III2IV respiratory supercomplex from Saccharomyces cerevisiae
8YHQ 2.42 Å, Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in pyraclostrobin-bound state
1P84 2.5 Å, HDBT inhibited Yeast Cytochrome bc1 Complex
3CXH 2.5 Å, Structure of yeast complex III with isoform-2 cytochrome c bound and definition of a…
8ZJC 2.5 Å, Cryo-EM structure of Saccharomyces cerevisiae bc1 complex
8ZMT 2.52 Å, Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in Metyltetraprole-bound state
9BPB 2.57 Å, Tethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae

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