6T0B: Cytochrome b-c1 complex subunit 1, mitochondrial

The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae. Determined by electron microscopy at 2.8 Å resolution. Released 22 Apr 2020.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 46
Atoms: 64,478
Mol. weight: 986.08 kDa
Ligands: ZN, CUA, MG, CA
Released: 22 Apr 2020

Explore 6T0B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T0B contains 402 α-helices and 172 β-strands across 46 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: 34 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	73-80	8
α-helix	81-88	8
α-helix	96-104	9
α-helix	106-118	13
α-helix	143-171	29
α-helix	179-181	3
α-helix	184-215	32
α-helix	229-263	35
α-helix	270-283	14
α-helix	288-291	4
α-helix	299-310	12
α-helix	313-327	15
α-helix	336-358	23
α-helix	361-364	4
β-strand	370	1	51
α-helix	371-379	9
α-helix	380-385	6
α-helix	386-401	16
α-helix	404-406	3
α-helix	407-425	19
α-helix	427-434	8
α-helix	436	1
β-strand	437	1	51
α-helix	445-447	3
α-helix	448-478	31
α-helix	481-484	4
α-helix	494-496	3
α-helix	504-506	3
α-helix	514-516	3
α-helix	519	1
α-helix	530-531	2
β-strand	532-533	2	52

Chain A: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	29-32	4	1
β-strand	37-42	6	1
β-strand	49-55	7	1
α-helix	59-61	3
α-helix	69-77	9
α-helix	80-89	10
β-strand	92-97	6	1
β-strand	102-108	7	1
α-helix	113-120	8
α-helix	121-125	5
α-helix	137-152	16
α-helix	156-168	13
α-helix	173-175	3
α-helix	182-186	5
α-helix	191-200	10
β-strand	206-212	7	1
α-helix	216-225	10
α-helix	235-238	4
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	302-306	5
β-strand	314-321	8	2
β-strand	326-334	9	2
α-helix	340-356	17
α-helix	360-378	19
α-helix	383-397	15
α-helix	404-410	7
α-helix	415-425	11
β-strand	432-437	6	2
α-helix	445-449	5
α-helix	450-452	3

Chain b: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-64	34
α-helix	79-82	4
α-helix	84-107	24
β-strand	115-122	8	53
β-strand	125-130	6	53
β-strand	141-145	5	53
α-helix	146	1
β-strand	147	1	54
α-helix	148-149	2
α-helix	150-152	3
α-helix	157-158	2
β-strand	163	1	54
β-strand	167-170	4	55
β-strand	174-181	8	53
β-strand	186-190	5	56
β-strand	195-199	5	56
β-strand	205-210	6	53
β-strand	215-220	6	55
β-strand	233-239	7	55
α-helix	241-248	8

Chain B: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	3
β-strand	28-35	8	3
α-helix	39-41	3
α-helix	47-54	8
β-strand	59	1	4
α-helix	64-74	11
β-strand	76-82	7	3
β-strand	87-94	8	3
α-helix	95-97	3
α-helix	98-110	13
β-strand	112	1	4
α-helix	116-118	3
α-helix	119-123	5
α-helix	124-135	12
α-helix	138-150	13
α-helix	169-179	11
α-helix	182-184	3
β-strand	185-190	6	3
α-helix	194-201	8
α-helix	206-208	3
β-strand	228-232	5	5
β-strand	237-245	9	5
α-helix	250-260	11
β-strand	273-279	7	5
β-strand	282-291	10	5
α-helix	294-308	15
β-strand	312-313	2	6
α-helix	315-317	3
α-helix	318-328	11
β-strand	345-346	2	6
β-strand	352-357	6	5
α-helix	365-367	3

Chain c: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	57
α-helix	3-6	4
α-helix	17-19	3
α-helix	22-40	19
α-helix	49-74	26
α-helix	81-113	33
α-helix	126	1
α-helix	131-133	3
α-helix	137-160	24
α-helix	165-190	26
α-helix	199-231	33
α-helix	241-261	21
α-helix	262-267	6

Chain C: 23 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-13	5
α-helix	14-18	5
β-strand	21-23	3	7
α-helix	28-31	4
α-helix	32-51	20
α-helix	61-70	10
β-strand	72	1	8
α-helix	75-102	28
α-helix	111-134	24
β-strand	137	1	9
α-helix	138-148	11
α-helix	149-153	5
α-helix	158-166	9
α-helix	173-202	30
β-strand	218-220	3	7
α-helix	225-245	21
α-helix	254-257	4
β-strand	259	1	9
α-helix	260	1
α-helix	273-275	3
α-helix	276-284	9
α-helix	288-300	13
α-helix	301-303	3
α-helix	305-308	4
β-strand	313	1	10
α-helix	320-339	20
α-helix	346-361	16
α-helix	362-366	5
α-helix	367-380	14

Chain d: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	37-39	3
α-helix	49-51	3
α-helix	56-58	3
α-helix	59-62	4
α-helix	65-76	12
β-strand	98-102	5	58
β-strand	106	1	59
β-strand	109-111	3	52
β-strand	122-124	3	52
β-strand	127	1	59
β-strand	132-133	2	58
β-strand	140-145	6	58

Chain D: 16 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	64-67	4
α-helix	69-71	3
α-helix	87-99	13
α-helix	101-103	3
β-strand	107-111	5	11
β-strand	116	1	12
β-strand	120	1	12
α-helix	122-130	9
β-strand	133-136	4	13
α-helix	137-138	2
β-strand	145-148	4	13
β-strand	154-155	2	11
α-helix	156-157	2
α-helix	162-168	7
α-helix	174-176	3
α-helix	177-179	3
α-helix	188-195	8
α-helix	208-209	2
β-strand	213-214	2	14
β-strand	222-223	2	14
α-helix	244-259	16
α-helix	263-291	29
α-helix	293-296	4
β-strand	299-302	4	2
α-helix	303-307	5

38 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, L	protein	431	Saccharomyces cerevisiae S288c	P07256 (AlphaFold model)
Cytochrome b-c1 complex subunit 2, mitochondrial	B, M	protein	352	Saccharomyces cerevisiae S288c	P07257 (AlphaFold model)
Cytochrome b	C, N	protein	385	Saccharomyces cerevisiae S288c	P00163 (AlphaFold model)
Cytochrome c1, heme protein, mitochondrial	D, O	protein	248	Saccharomyces cerevisiae S288c	P07143 (AlphaFold model)
Cytochrome b-c1 complex subunit Rieske, mitochondrial	E, P	protein	185	Saccharomyces cerevisiae S288c	P08067
Cytochrome b-c1 complex subunit 6	F, Q	protein	147	Saccharomyces cerevisiae S288c	P00127
Cytochrome b-c1 complex subunit 7	G, R	protein	127	Saccharomyces cerevisiae S288c	P00128
Cytochrome b-c1 complex subunit 8	H, S	protein	94	Saccharomyces cerevisiae S288c	P08525
Cytochrome b-c1 complex subunit 9	I, T	protein	66	Saccharomyces cerevisiae S288c	P22289
Cytochrome b-c1 complex subunit 10	J, U	protein	77	Saccharomyces cerevisiae S288c	P37299
Cytochrome c oxidase subunit 1	a, n	protein	534	Saccharomyces cerevisiae S288c	P00401
Cytochrome c oxidase subunit 2	b, o	protein	236	Saccharomyces cerevisiae S288c	P00410

11 more molecules are not listed.

Sequence of entity 1 (A, L), FASTA

>6T0B_1 Cytochrome b-c1 complex subunit 1, mitochondrial (chains A, L)
AEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVA
AKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLK
QVQDFEENDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNA
VVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVE
GEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSG
LWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVND
ANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYM
RIRSDMSMMRW

Sequence of entity 2 (B, M), FASTA

>6T0B_2 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B, M)
LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGG
TFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ
CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEAD
LKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL
ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSP
AINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL

Sequence of entity 3 (C, N), FASTA

>6T0B_3 Cytochrome b (chains C, N)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK

Sequence of entity 4 (D, O), FASTA

>6T0B_4 Cytochrome c1, heme protein, mitochondrial (chains D, O)
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHT
NEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIV
KARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTP
ATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV
FNPPKPRK

Sequence of entity 5 (E, P), FASTA

>6T0B_5 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains E, P)
KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLA
MAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDP
QWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGD
KVIVG

Sequence of entity 6 (F, Q), FASTA

>6T0B_6 Cytochrome b-c1 complex subunit 6 (chains F, Q)
MGMLELVGEYWEQLKITVVPVVAAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDD
DDDDDEDEEEEEEVTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHK
EDCVEEFFHLQHYLDTATAPRLFDKLK

Sequence of entity 7 (G, R), FASTA

>6T0B_7 Cytochrome b-c1 complex subunit 7 (chains G, R)
MPQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTAL
RRLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDEL
DNIEVSK

Sequence of entity 8 (H, S), FASTA

>6T0B_8 Cytochrome b-c1 complex subunit 8 (chains H, S)
MGPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVL
IPAGIYWYWWKNGNEYNEFLYSKAGREELERVNV

Sequence of entity 9 (I, T), FASTA

>6T0B_9 Cytochrome b-c1 complex subunit 9 (chains I, T)
MSFSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAAGD
GDDDDE

Sequence of entity 10 (J, U), FASTA

>6T0B_10 Cytochrome b-c1 complex subunit 10 (chains J, U)
MAYTSHLSSKTGLHFGRLSLRSLTAYAPNLMLWGGASMLGLFVFTEGWPKFQDTLYKKIP
LLGPTLEDHTPPEDKPN

Sequence of entity 11 (a, n), FASTA

>6T0B_11 Cytochrome c oxidase subunit 1 (chains a, n)
MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVV
GHAVLMIFFLVMPALIGGFGNYLLPLMIGATDTAFPRINNIAFWVLPMGLVCLVTSTLVE
SGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMH
KLPLFVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFG
HPEVYILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDAD
TRAYFTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALAN
ASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIG
ANVIFFPMHFLGINGMPRRIPDYPDAFAGWNYVASIGSFIATLSLFLFIYILYDQLVNGL
NNKVNNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS

Sequence of entity 12 (b, o), FASTA

>6T0B_12 Cytochrome c oxidase subunit 2 (chains b, o)
DVPTPYACYFQDSATPNQEGILELHDNIMFYLLVILGLVSWMLYTIVMTYSKNPIAYKYI
KHGQTIEVIWTIFPAVILLIIAFPSFILLYLCDEVISPAMTIKAIGYQWYWKYEYSDFIN
DSGETVEFESYVIPDELLEEGQLRLLDTDTSMVVPVDTHIRFVVTAADVIHDFAIPSLGI
KVDATPGRLNQVSALIQREGVFYGACSELCGTGHANMPIKIEAVSLPKFLEWLNEQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
CUA	Dinuclear copper ion	Cu2	2
MG	Magnesium ion	Mg	2
CA	Calcium ion	Ca	2
HEA	Heme-a	C49 H56 Fe N4 O6	4
CU	Copper (II) ion	Cu	2
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
HEC	Heme C	C34 H36 Fe N4 O4	2
PCF	1,2-diacyl-sn-glycero-3-phoshocholine	C40 H80 N O8 P	7
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4
PEF	Di-palmitoyl-3-sn-phosphatidylethanolamine	C37 H74 N O8 P	26
CDL	Cardiolipin	C81 H156 O17 P2	8

Primary citation

Rcf2 revealed in cryo-EM structures of hypoxic isoforms of mature mitochondrial III-IV supercomplexes. Hartley, A.M., Meunier, B., Pinotsis, N. et al. Proc Natl Acad Sci U S A (2020) 117:9329-9337. DOI 10.1073/pnas.1920612117 · 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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