8E7S: Cytochrome b-c1 complex subunit 1, mitochondrial

III2IV2 respiratory supercomplex from Saccharomyces cerevisiae with 4 bound UQ6. Determined by electron microscopy at 3.2 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae
Chains: 44
Atoms: 62,847
Mol. weight: 997.88 kDa
Ligands: FES, CDL, CN5, HEM
Released: 24 May 2023

Explore 8E7S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E7S contains 356 α-helices and 161 β-strands across 44 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: 17 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	29-30	2	44
β-strand	34	1	45
β-strand	36	1	45
β-strand	38-39	2	46
β-strand	40-41	2	44
β-strand	42	1	47
β-strand	50-53	4	48
β-strand	54-55	2	49
α-helix	69-76	8
α-helix	77-81	5
α-helix	82-88	7
β-strand	94-96	3	48
β-strand	103-107	5	48
α-helix	113-120	8
α-helix	121-125	5
α-helix	134-153	20
α-helix	157-168	12
α-helix	182-185	4
α-helix	191-200	10
β-strand	206-207	2	49
β-strand	208-209	2	46
β-strand	212	1	47
α-helix	217-221	5
β-strand	259	1	50
β-strand	261	1	51
β-strand	265-266	2	52
α-helix	275-281	7
β-strand	288-289	2	53
α-helix	301-306	6
β-strand	314-315	2	53
β-strand	319-321	3	52
β-strand	326-328	3	52
β-strand	332	1	51
α-helix	340-353	14
α-helix	360-378	19
α-helix	383-396	14
α-helix	403-411	9
α-helix	415-425	11
β-strand	437	1	50

Chain A: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	1
β-strand	34	1	2
β-strand	36	1	2
β-strand	37-40	4	1
β-strand	42	1	3
β-strand	50-51	2	4
β-strand	52-55	4	1
α-helix	59-61	3
α-helix	69-76	8
α-helix	77-81	5
α-helix	82-88	7
β-strand	93	1	4
β-strand	106-107	2	4
α-helix	113-123	11
α-helix	134-154	21
α-helix	157-168	12
α-helix	182-186	5
α-helix	191-200	10
β-strand	206-209	4	1
β-strand	212	1	3
α-helix	217-221	5
α-helix	235-238	4
β-strand	247-248	2	5
β-strand	261-266	6	6
α-helix	275-283	9
β-strand	288-289	2	7
α-helix	301-307	7
β-strand	314-315	2	7
β-strand	316-320	5	6
β-strand	327-332	6	6
α-helix	340-356	17
α-helix	360-378	19
α-helix	383-396	14
α-helix	403-410	8
α-helix	415-425	11
β-strand	432-433	2	5
α-helix	439-441	3

Chain b: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	54
β-strand	29-35	7	54
α-helix	45-47	3
α-helix	48-53	6
α-helix	69-74	6
β-strand	77-80	4	54
β-strand	87-93	7	54
α-helix	98-108	11
α-helix	116-118	3
α-helix	124-136	13
α-helix	138-151	14
α-helix	169-179	11
β-strand	187-190	4	54
α-helix	194-200	7
α-helix	205-208	4
α-helix	220-222	3
β-strand	228-230	3	55
β-strand	238	1	56
β-strand	241-244	4	55
α-helix	251-261	11
β-strand	271-273	3	57
β-strand	276-277	2	55
β-strand	284-287	4	55
β-strand	288-289	2	57
β-strand	290	1	56
α-helix	296-308	13
α-helix	315-317	3
α-helix	318-328	11
α-helix	334-337	4
β-strand	352-355	4	55
β-strand	356	1	56
α-helix	363-364	2

Chain B: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	8
β-strand	29-35	7	8
α-helix	45-47	3
α-helix	48-53	6
α-helix	69-74	6
β-strand	76-80	5	8
β-strand	87-93	7	8
α-helix	98-108	11
α-helix	116-118	3
α-helix	124-135	12
α-helix	138-151	14
α-helix	169-179	11
β-strand	187-190	4	8
α-helix	194-200	7
α-helix	205-207	3
α-helix	220-222	3
β-strand	228-230	3	9
β-strand	237-246	10	9
α-helix	247-249	3
α-helix	251-261	11
β-strand	271	1	10
β-strand	276-278	3	9
β-strand	282-287	6	9
β-strand	289	1	10
β-strand	290-291	2	9
α-helix	296-310	15
α-helix	318-328	11
β-strand	352-356	5	9

Chain c: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	50-81	32
α-helix	87-89	3
β-strand	94-97	4	58
β-strand	106-111	6	59
β-strand	114-120	7	59
α-helix	123-130	8
α-helix	134-136	3
α-helix	143-146	4
β-strand	152-156	5	59
β-strand	159	1	60
β-strand	163	1	60
α-helix	165-166	2
β-strand	167-168	2	61
β-strand	176-178	3	61
β-strand	183-185	3	61
β-strand	191-193	3	61
α-helix	200-204	5
β-strand	205-207	3	58
β-strand	211-214	4	58

Chain C: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	12
α-helix	44-45	2
α-helix	52-80	29
β-strand	94-97	4	13
α-helix	98-100	3
β-strand	106-111	6	14
β-strand	114-119	6	14
α-helix	123-130	8
α-helix	134-136	3
β-strand	153-155	3	14
α-helix	165-166	2
β-strand	167-168	2	15
β-strand	176-177	2	15
β-strand	184-185	2	15
β-strand	191	1	15
α-helix	199-204	6
β-strand	206-208	3	13
β-strand	211-214	4	13

Chain d: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	62
β-strand	18-19	2	62
α-helix	20-44	25
α-helix	52-55	4

Chain D: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	16
β-strand	14	1	17
β-strand	19	1	17
α-helix	20-44	25
α-helix	49-58	10

31 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 10, mitochondrial	D, d	protein	77	Saccharomyces cerevisiae	P37299 (AlphaFold model)
Cytochrome b-c1 complex subunit 9, mitochondrial	E, e	protein	66	Saccharomyces cerevisiae	P22289
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, 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, m	protein	78	Saccharomyces cerevisiae	P04039

10 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA

>8E7S_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

>8E7S_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

>8E7S_3 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains C, c)
MLGIRSSVKTCFKPMSLTSKRLISQSLLASKSTYRTPNFDDVLKENNDADKGRSYAYFMV
GAMGLLSSAGAKSTVETFISSMTATADVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRH
RTPHEIQEANSVDMSALKDPQTDADRVKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPC
HGSHYDISGRIRKGPAPLNLEIPAYEFDGDKVIVG

Sequence of entity 4 (D, d), FASTA

>8E7S_4 Cytochrome b-c1 complex subunit 10, mitochondrial (chains D, d)
MAYTSHLSSKTGLHFGRLSLRSLTAYAPNLMLWGGASMLGLFVFTEGWPKFQDTLYKKIP
LLGPTLEDHTPPEDKPN

Sequence of entity 5 (E, e), FASTA

>8E7S_5 Cytochrome b-c1 complex subunit 9, mitochondrial (chains E, e)
MSFSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAAGD
GDDDDE

Sequence of entity 6 (F, f), FASTA

>8E7S_6 Cytochrome b-c1 complex subunit 7, mitochondrial (chains F, f)
MPQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTAL
RRLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDEL
DNIEVSK

Sequence of entity 7 (G, g), FASTA

>8E7S_7 Cytochrome b-c1 complex subunit 6, mitochondrial (chains G, g)
MGMLELVGEYWEQLKITVVPVVAAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDD
DDDDDEDEEEEEEVTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHK
EDCVEEFFHLQHYLDTATAPRLFDKLK

Sequence of entity 8 (H, h), FASTA

>8E7S_8 Cytochrome b-c1 complex subunit 8, mitochondrial (chains H, h)
MGPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVL
IPAGIYWYWWKNGNEYNEFLYSKAGREELERVNV

Sequence of entity 9 (J, j), FASTA

>8E7S_9 Cytochrome b (chains J, j)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK

Sequence of entity 10 (K, k), FASTA

>8E7S_10 Cytochrome c oxidase subunit 1 (chains K, k)
MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVV
GHAVLMIFFLVMPALIGGFGNYLLPLMIGATDTAFPRINNIAFWVLPMGLVCLVTSTLVE
SGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMH
KLPLFVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFG
HPEVYILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDAD
TRAYFTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALAN
ASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIG
ANVIFFPMHFLGINGMPRRIPDYPDAFAGWNYVASIGSFIATLSLFLFIYILYDQLVNGL
NNKVNNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS

Sequence of entity 11 (L, l), FASTA

>8E7S_11 Cytochrome c1, heme protein, mitochondrial (chains L, l)
MFSNLSKRWAQRTLSKSFYSTATGAASKSGKLTQKLVTAGVAAAGITASTLLYADSLTAE
AMTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSH
TNEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLI
VKARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGT
PATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKF
VFNPPKPRK

Sequence of entity 12 (M, m), FASTA

>8E7S_12 Cytochrome c oxidase subunit 8, mitochondrial (chains M, m)
MLCQQMIRTTAKRSSNIMTRPIIMKRSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIG
FAVPFVACYVQLKKSGAF

Ligands and cofactors

ID	Name	Formula	Copies
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
CDL	Cardiolipin	C81 H156 O17 P2	10
CN5	(5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-dipho…	C26 H52 O13 P2	1
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	4
CU	Copper (II) ion	Cu	2
CUA	Dinuclear copper ion	Cu2	4
HEA	Heme-a	C49 H56 Fe N4 O6	4
PCF	1,2-diacyl-sn-glycero-3-phoshocholine	C40 H80 N O8 P	6
PEF	Di-palmitoyl-3-sn-phosphatidylethanolamine	C37 H74 N O8 P	24

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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