3CX5: Cytochrome b-c1 complex subunit 1, mitochondrial

Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer. Determined by X-ray diffraction at 1.9 Å resolution. Released 13 May 2008.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Saccharomyces cerevisiae, Mus musculus
Chains: 23
Atoms: 38,020
Mol. weight: 534.17 kDa
Ligands: 6PH, UMQ, HEM, SMA
Released: 13 May 2008

Explore 3CX5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3CX5 contains 244 α-helices and 163 β-strands across 23 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: 23 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	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	80-88	9
β-strand	92-97	6	1
β-strand	102-108	7	1
α-helix	113-121	9
α-helix	122-126	5
α-helix	134-154	21
α-helix	156-168	13
α-helix	173-175	3
α-helix	182-186	5
α-helix	190-200	11
α-helix	203-205	3
β-strand	206-212	7	1
α-helix	216-223	8
α-helix	234-237	4
α-helix	240-242	3
β-strand	247-252	6	2
β-strand	259-266	8	2
α-helix	275-285	11
β-strand	287-289	3	2
α-helix	295-297	3
α-helix	302-307	6
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	403-412	10
α-helix	415-425	11
β-strand	432-437	6	2
α-helix	445-450	6

Chain B: 21 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	77-82	6	3
β-strand	87-94	8	3
α-helix	95-97	3
α-helix	98-111	14
β-strand	112	1	4
α-helix	116-118	3
α-helix	119-123	5
α-helix	124-135	12
α-helix	138-151	14
α-helix	169-179	11
α-helix	182-184	3
β-strand	185-190	6	3
α-helix	194-203	10
α-helix	220-222	3
β-strand	228-232	5	5
β-strand	237-245	9	5
α-helix	250-261	12
α-helix	268-270	3
β-strand	273-279	7	5
β-strand	282-291	10	5
α-helix	294-309	16
β-strand	312-313	2	6
α-helix	315-317	3
α-helix	318-328	11
α-helix	340-342	3
β-strand	345-346	2	6
β-strand	352-357	6	5
α-helix	359-361	3
α-helix	365-367	3

Chain C: 24 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	10-13	4
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
α-helix	75-103	29
α-helix	111-135	25
β-strand	137	1	8
α-helix	138-149	12
α-helix	150-153	4
α-helix	158-166	9
α-helix	173-204	32
β-strand	218-220	3	7
α-helix	221-225	5
α-helix	226-246	21
α-helix	254-257	4
β-strand	259	1	8
α-helix	273-275	3
α-helix	276-283	8
α-helix	288-300	13
α-helix	301-304	4
α-helix	305-308	4
α-helix	320-340	21
α-helix	348-361	14
α-helix	362-366	5
α-helix	367-380	14

Chain D: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	64-67	4
α-helix	69-72	4
α-helix	83-85	3
α-helix	87-99	13
α-helix	101-103	3
β-strand	111	1	9
α-helix	112-115	4
β-strand	116	1	10
β-strand	120	1	10
α-helix	122-129	8
β-strand	133-135	3	11
β-strand	146-148	3	11
β-strand	154	1	9
α-helix	155-157	3
α-helix	162-167	6
α-helix	174-176	3
α-helix	187-196	10
α-helix	202-203	2
α-helix	208-209	2
β-strand	213-214	2	12
β-strand	222-223	2	12
α-helix	226-227	2
α-helix	244-259	16
α-helix	263-296	34
β-strand	299-302	4	2
α-helix	304-306	3

Chain E: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
β-strand	43	1	13
α-helix	44-45	2
α-helix	51-80	30
α-helix	86-88	3
β-strand	94-97	4	14
α-helix	98-100	3
β-strand	106-111	6	15
β-strand	114-120	7	15
α-helix	123-130	8
α-helix	134-136	3
β-strand	152-156	5	15
α-helix	166	1
β-strand	167-170	4	16
β-strand	175-178	4	16
β-strand	183-185	3	16
β-strand	191-193	3	16
α-helix	199-204	6
β-strand	205-208	4	14
β-strand	211-214	4	14

Chain F: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	77-86	10
α-helix	89-110	22
α-helix	114-116	3
α-helix	124-142	19
α-helix	143-145	3

Chain G: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	5-17	13
α-helix	19-36	18
α-helix	38-41	4
α-helix	45-48	4
α-helix	54-62	9
α-helix	65-83	19
α-helix	90-92	3
α-helix	94-95	2
α-helix	96-98	3
α-helix	104-121	18

Chain H: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	17
β-strand	15	1	17
α-helix	19-21	3
β-strand	24-29	6	2
α-helix	31-33	3
β-strand	34	1	13
α-helix	50-53	4
α-helix	56-80	25
α-helix	83-85	3
α-helix	86-93	8

14 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	P07256 (AlphaFold model)
Cytochrome b-c1 complex subunit 2, mitochondrial	B, M	protein	352	Saccharomyces cerevisiae	P07257 (AlphaFold model)
Cytochrome B	C, N	protein	385	Saccharomyces cerevisiae	P00163 (AlphaFold model)
Cytochrome c1, heme protein, mitochondrial	D, O	protein	248	Saccharomyces cerevisiae	P07143 (AlphaFold model)
Cytochrome b-c1 complex subunit Rieske, mitochondrial	E, P	protein	185	Saccharomyces cerevisiae	P08067
Cytochrome b-c1 complex subunit 6	F, Q	protein	146	Saccharomyces cerevisiae	P00127
Cytochrome b-c1 complex subunit 7	G, R	protein	126	Saccharomyces cerevisiae	P00128
Cytochrome b-c1 complex subunit 8	H, S	protein	93	Saccharomyces cerevisiae	P08525
Cytochrome b-c1 complex subunit 9	I, T	protein	65	Saccharomyces cerevisiae	P22289
Heavy chain (VH) of fv-fragment	J, U	protein	127	Mus musculus
Light chain (VL) of fv-fragment	K, V	protein	107	Mus musculus
Cytochrome c iso-1	W	protein	108	Saccharomyces cerevisiae	P00044

Sequence of entity 1 (A, L), FASTA

>3CX5_1 Cytochrome b-c1 complex subunit 1, mitochondrial (chains A, L)
AEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVA
AKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLK
QVQDFEDNDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNA
VVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVE
GEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSG
LWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVND
ANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYM
RIRSDMSMMRW

Sequence of entity 2 (B, M), FASTA

>3CX5_2 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B, M)
LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGG
TFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ
CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEAD
LKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL
ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSP
AINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL

Sequence of entity 3 (C, N), FASTA

>3CX5_3 CYTOCHROME B (chains C, N)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK

Sequence of entity 4 (D, O), FASTA

>3CX5_4 Cytochrome c1, heme protein, mitochondrial (chains D, O)
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHT
NEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIV
KARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTP
ATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV
FNPPKPRK

Sequence of entity 5 (E, P), FASTA

>3CX5_5 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains E, P)
KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLA
MAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDP
QWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGD
KVIVG

Sequence of entity 6 (F, Q), FASTA

>3CX5_6 Cytochrome b-c1 complex subunit 6 (chains F, Q)
GMLELVGEYWEQLKITVVPVVAAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDDD
DDDDEDEEEEEEVTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKE
DCVEEFFHLQHYLDTATAPRLFDKLK

Sequence of entity 7 (G, R), FASTA

>3CX5_7 Cytochrome b-c1 complex subunit 7 (chains G, R)
PQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALR
RLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELD
NIEVSK

Sequence of entity 8 (H, S), FASTA

>3CX5_8 Cytochrome b-c1 complex subunit 8 (chains H, S)
GPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLI
PAGIYWYWWKNGNEYNEFLYSKAGREELERVNV

Sequence of entity 9 (I, T), FASTA

>3CX5_9 Cytochrome b-c1 complex subunit 9 (chains I, T)
SFSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAAGDG
DDDDE

Sequence of entity 10 (J, U), FASTA

>3CX5_10 HEAVY CHAIN (VH) OF FV-FRAGMENT (chains J, U)
EVKLQESGAGLVQPSQSLSLTCSVTGYSITSGYYWNWIRLFPGNKLEWVGYISNVGDNNY
NPSLKDRLSITRDTSKNQFFLKLNSVTTEDTATYYCARSEYYSVTGYAMDYWGQGTTVTV
SSAWRHP

Sequence of entity 11 (K, V), FASTA

>3CX5_11 LIGHT CHAIN (VL) OF FV-FRAGMENT (chains K, V)
DIELTQTPVSLAASLGDRVTISCRASQDINNFLNWYQQKPDGTIKLLIYYTSRLHAGVPS
RFSGSGSGTDYSLTISNLEPEDIATYFCQHHIKFPWTFGAGTKLEIK

Sequence of entity 12 (W), FASTA

>3CX5_12 Cytochrome c iso-1 (chains W)
TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK
NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

Ligands and cofactors

ID	Name	Formula	Copies
6PH	(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate	C31 H61 O8 P	2
UMQ	Undecyl-maltoside	C23 H44 O11	2
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	7
SMA	Stigmatellin a	C30 H42 O7	2
8PE	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl…	C37 H74 N O8 P	2
9PE	(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]et…	C30 H60 N O8 P	2
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
7PH	(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate	C29 H57 O8 P	2
CN3	(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(prop…	C36 H68 O17 P2	2
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2

Primary citation

Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer. Solmaz, S.R., Hunte, C. J Biol Chem (2008) 283:17542-17549. DOI 10.1074/jbc.M710126200 · PubMed

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

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
8YIL 2.58 Å, Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF24228-bound state

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