1KYO: PDB entry 1KYO

Yeast cytochrome BC1 complex with bound substrate cytochrome C. Determined by X-ray diffraction at 2.97 Å resolution. Released 6 Mar 2002.

Method: X-ray diffraction
Resolution: 2.97 Å
Organisms: Saccharomyces cerevisiae, Mus musculus
Chains: 23
Atoms: 35,643
Mol. weight: 507.23 kDa
Ligands: FES, SMA, HEC
Released: 6 Mar 2002

Explore 1KYO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1KYO contains 216 α-helices and 165 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	1
β-strand	37-42	6	1
β-strand	48-54	7	1
α-helix	58-60	3
α-helix	68-76	9
α-helix	79-88	10
β-strand	91-96	6	1
β-strand	101-107	7	1
α-helix	112-120	9
α-helix	121-125	5
α-helix	136-142	7
α-helix	144-153	10
α-helix	155-167	13
α-helix	172-174	3
α-helix	181-186	6
α-helix	189-199	11
β-strand	205-211	7	1
α-helix	215-224	10
β-strand	246-251	6	2
β-strand	252	1	3
β-strand	258-265	8	2
α-helix	267-268	2
α-helix	274-284	11
β-strand	286-288	3	2
α-helix	292-295	4
α-helix	301-306	6
β-strand	313-320	8	2
β-strand	325-333	9	2
α-helix	339-355	17
α-helix	359-377	19
α-helix	382-395	14
α-helix	402-410	9
α-helix	414-424	11
β-strand	431-436	6	2
α-helix	442-443	2
α-helix	444-449	6

Chain B: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	18-20	3	4
β-strand	29-35	7	4
α-helix	47-54	8
β-strand	59	1	5
β-strand	62	1	5
α-helix	64-74	11
β-strand	79-82	4	4
β-strand	87-93	7	4
α-helix	95-97	3
α-helix	98-111	14
β-strand	112	1	5
α-helix	116-118	3
α-helix	119-123	5
α-helix	124-134	11
α-helix	138-150	13
α-helix	169-179	11
α-helix	182-184	3
β-strand	185-190	6	4
α-helix	194-201	8
α-helix	212-214	3
β-strand	228-232	5	6
β-strand	238-245	8	6
α-helix	250-259	10
β-strand	273-278	6	6
β-strand	283-290	8	6
α-helix	294-309	16
α-helix	324-327	4
β-strand	352-357	6	6
α-helix	359-361	3

Chain C: 23 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-13	6
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	75-102	28
α-helix	111-135	25
β-strand	137	1	8
α-helix	138-148	11
α-helix	149-153	5
α-helix	158-166	9
α-helix	173-204	32
β-strand	218-220	3	7
α-helix	225-246	22
α-helix	254-257	4
β-strand	259	1	8
α-helix	273-275	3
α-helix	276-284	9
α-helix	288-300	13
α-helix	301-304	4
α-helix	305-308	4
β-strand	313	1	9
α-helix	320-341	22
α-helix	346-361	16
α-helix	362-366	5
α-helix	367-380	14

Chain D: 13 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	10
α-helix	112-115	4
β-strand	116	1	11
β-strand	120	1	11
α-helix	122-129	8
β-strand	133-136	4	12
β-strand	145-148	4	12
β-strand	154	1	10
α-helix	155-157	3
α-helix	162-167	6
α-helix	188-196	9
α-helix	202-203	2
β-strand	213-214	2	13
β-strand	222-223	2	13
α-helix	244-259	16
α-helix	263-297	35
β-strand	299-302	4	2

Chain E: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	14
α-helix	52-79	28
α-helix	86-88	3
β-strand	94-97	4	15
β-strand	106-111	6	16
β-strand	114-120	7	16
α-helix	123-130	8
α-helix	134-136	3
α-helix	143-146	4
β-strand	152-156	5	16
α-helix	166	1
β-strand	167-170	4	17
β-strand	175-178	4	17
β-strand	183-185	3	17
β-strand	191	1	17
β-strand	201	1	16
β-strand	205-207	3	15
β-strand	211-214	4	15

Chain F: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	77-86	10
α-helix	89-108	20
α-helix	124-142	19
α-helix	143-145	3

Chain G: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-17	13
α-helix	19-36	18
α-helix	38-41	4
α-helix	45-48	4
β-strand	49	1	9
α-helix	54-62	9
α-helix	65-83	19
α-helix	90-92	3
α-helix	94-95	2
α-helix	104-122	19

Chain H: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
β-strand	22	1	3
β-strand	24-29	6	2
α-helix	31-33	3
β-strand	34	1	14
α-helix	56-80	25
α-helix	86-92	7

15 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
Ubiquinol-cytochrome C reductase complex core protein I	A, L	protein	430	Saccharomyces cerevisiae	P07256 (AlphaFold model)
Ubiquinol-cytochrome C reductase complex core protein 2	B, M	protein	352	Saccharomyces cerevisiae	P07257 (AlphaFold model)
Cytochrome B	C, N	protein	385	Saccharomyces cerevisiae	P00163 (AlphaFold model)
Cytochrome C1, heme protein	D, O	protein	248	Saccharomyces cerevisiae	P07143 (AlphaFold model)
Ubiquinol-cytochrome C reductase iron-sulfur subunit	E, P	protein	185	Saccharomyces cerevisiae	P08067
Ubiquinol-cytochrome C reductase complex 17 kd protein	F, Q	protein	74	Saccharomyces cerevisiae	P00127
Ubiquinol-cytochrome C reductase complex 14 kd protein	G, R	protein	126	Saccharomyces cerevisiae	P00128
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C	H, S	protein	93	Saccharomyces cerevisiae	P08525
Ubiquinol-cytochrome C reductase complex 7.3 kd protein	I, T	protein	57	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

>1KYO_1 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I (chains A, L)
AEVTQLSNGIVVATEHNPAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVAA
KEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLKQ
VQDFEDNDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNAV
VVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVEG
EPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSGL
WGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVNDA
NLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYMR
IRSDMSMMRW

Sequence of entity 2 (B, M), FASTA

>1KYO_2 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2 (chains B, M)
LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGG
TFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ
CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEAD
LKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL
ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSP
AINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL

Sequence of entity 3 (C, N), FASTA

>1KYO_3 CYTOCHROME B (chains C, N)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FTLTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK

Sequence of entity 4 (D, O), FASTA

>1KYO_4 CYTOCHROME C1, HEME PROTEIN (chains D, O)
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHT
NEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIV
KARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTP
ATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV
FNPPKPRK

Sequence of entity 5 (E, P), FASTA

>1KYO_5 UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT (chains E, P)
KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLA
MAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDP
QWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGD
KVIVG

Sequence of entity 6 (F, Q), FASTA

>1KYO_6 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN (chains F, Q)
DTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEEFFHLQHY
LDTATAPRLFDKLK

Sequence of entity 7 (G, R), FASTA

>1KYO_7 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN (chains G, R)
PQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALR
RLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELD
NIEVSK

Sequence of entity 8 (H, S), FASTA

>1KYO_8 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C (chains H, S)
GPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLI
PAGIYWYWWKNGNEYNEFLYSKAGREELERVNV

Sequence of entity 9 (I, T), FASTA

>1KYO_9 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN (chains I, T)
SFSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKAKIAA

Sequence of entity 10 (J, U), FASTA

>1KYO_10 HEAVY CHAIN (VH) OF FV-FRAGMENT (chains J, U)
EVKLQESGAGLVQPSQSLSLTCSVTGYSITSGYYWNWIRLFPGNKLEWVGYISNVGDNNY
NPSLKDRLSITRDTSKNQFFLKLNSVTTEDTATYYCARSEYYSVTGYAMDYWGQGTTVTV
SSAWRHP

Sequence of entity 11 (K, V), FASTA

>1KYO_11 LIGHT CHAIN (VL) OF FV-FRAGMENT (chains K, V)
DIELTQTPVSLAASLGDRVTISCRASQDINNFLNWYQQKPDGTIKLLIYYTSRLHAGVPS
RFSGSGSGTDYSLTISNLEPEDIATYFCQHHIKFPWTFGAGTKLEIK

Sequence of entity 12 (W), FASTA

>1KYO_12 CYTOCHROME C, ISO-1 (chains W)
TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKK
NVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE

Ligands and cofactors

ID	Name	Formula	Copies
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
SMA	Stigmatellin a	C30 H42 O7	2
HEC	Heme C	C34 H36 Fe N4 O4	7

Primary citation

Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c. Lange, C., Hunte, C. Proc Natl Acad Sci U S A (2002) 99:2800-2805. DOI 10.1073/pnas.052704699 · 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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