1KB9: Yeast cytochrome BC1 complex

Yeast cytochrome BC1 complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 18 Sept 2002.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Saccharomyces cerevisiae, Mus musculus
Chains: 11
Atoms: 18,040
Mol. weight: 252.22 kDa
Ligands: HEM, SMA, UQ6, PIE
Released: 18 Sept 2002

Explore 1KB9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1KB9 contains 119 α-helices and 80 β-strands across 11 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: 22 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	1
β-strand	37-41	5	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	110-112	3
α-helix	115-121	7
α-helix	122-126	5
α-helix	136-154	19
α-helix	156-168	13
α-helix	173-175	3
α-helix	182-185	4
α-helix	190-200	11
β-strand	206-211	6	1
α-helix	216-225	10
α-helix	236-238	3
β-strand	247-252	6	2
β-strand	253	1	3
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	403-411	9
α-helix	415-425	11
β-strand	432-437	6	2
α-helix	445-450	6

Chain B: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	4
β-strand	28-35	8	4
α-helix	39-41	3
α-helix	47-54	8
β-strand	59	1	5
α-helix	64-74	11
β-strand	76-82	7	4
β-strand	87-94	8	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	124-135	12
α-helix	138-150	13
α-helix	169-179	11
α-helix	182-184	3
β-strand	185-190	6	4
α-helix	194-202	9
α-helix	220-221	2
β-strand	228-232	5	6
β-strand	237-245	9	6
α-helix	246	1
α-helix	250-260	11
α-helix	266-270	5
β-strand	273-278	6	6
β-strand	283-291	9	6
α-helix	294-309	16
α-helix	320-324	5
α-helix	329-331	3
β-strand	352-357	6	6
α-helix	359-361	3

Chain C: 25 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	111-134	24
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	226-241	16
α-helix	242-246	5
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	346-361	16
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	122-130	9
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	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
α-helix	143-146	4
β-strand	152-156	5	15
α-helix	164-166	3
β-strand	167-168	2	16
β-strand	174-178	5	16
β-strand	183-186	4	16
β-strand	191-193	3	16
α-helix	199-201	3
β-strand	205-208	4	14
β-strand	211-214	4	14

Chain F: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	77-86	10
α-helix	89-109	21
α-helix	124-138	15
α-helix	142-145	4

Chain G: 9 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	104-121	18

Chain H: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	12	1	17
β-strand	15	1	17
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	13
α-helix	35-36	2
α-helix	56-80	25
α-helix	86-92	7

3 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	protein	431	Saccharomyces cerevisiae	P07256 (AlphaFold model)
Ubiquinol-cytochrome C reductase complex core protein 2	B	protein	352	Saccharomyces cerevisiae	P07257 (AlphaFold model)
Cytochrome B	C	protein	385	Saccharomyces cerevisiae	P00163 (AlphaFold model)
Cytochrome C1, heme protein	D	protein	246	Saccharomyces cerevisiae	P07143 (AlphaFold model)
Ubiquinol-cytochrome C reductase iron-sulfur subunit	E	protein	185	Saccharomyces cerevisiae	P08067
Ubiquinol-cytochrome C reductase complex 17 kd protein	F	protein	74	Saccharomyces cerevisiae	P00127
Ubiquinol-cytochrome C reductase complex 14 kd protein	G	protein	125	Saccharomyces cerevisiae	P00128
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C	H	protein	93	Saccharomyces cerevisiae	P08525
Ubiquinol-cytochrome C reductase complex 7.3 kd protein	I	protein	55	Saccharomyces cerevisiae	P22289
Heavy chain (VH) of fv-fragment	J	protein	127	Mus musculus
Light chain (VL) of fv-fragment	K	protein	107	Mus musculus

Sequence of entity 1 (A), FASTA

>1KB9_1 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I (chains A)
AEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVA
AKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLK
QVQDFEDNDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNA
VVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVE
GEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSG
LWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVND
ANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYM
RIRSDMSMMRW

Sequence of entity 2 (B), FASTA

>1KB9_2 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2 (chains B)
LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGG
TFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ
CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEAD
LKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL
ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSP
AINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL

Sequence of entity 3 (C), FASTA

>1KB9_3 CYTOCHROME B (chains C)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FTLTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK

Sequence of entity 4 (D), FASTA

>1KB9_4 CYTOCHROME C1, HEME PROTEIN (chains D)
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHT
NEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIV
KARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTP
ATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV
FNPPKP

Sequence of entity 5 (E), FASTA

>1KB9_5 UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT (chains E)
KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLA
MAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDP
QWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGD
KVIVG

Sequence of entity 6 (F), FASTA

>1KB9_6 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN (chains F)
VTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEEFFHLQHY
LDTATAPRLFDKLK

Sequence of entity 7 (G), FASTA

>1KB9_7 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN (chains G)
QSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALRR
LPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELDN
IEVSK

Sequence of entity 8 (H), FASTA

>1KB9_8 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C (chains H)
GPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLI
PAGIYWYWWKNGNEYNEFLYSKAGREELERVNV

Sequence of entity 9 (I), FASTA

>1KB9_9 UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN (chains I)
SSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAA

Sequence of entity 10 (J), FASTA

>1KB9_10 HEAVY CHAIN (VH) OF FV-FRAGMENT (chains J)
EVKLQESGAGLVQPSQSLSLTCSVTGYSITSGYYWNWIRLFPGNKLEWVGYISNVGDNNY
NPSLKDRLSITRDTSKNQFFLKLNSVTTEDTATYYCARSEYYSVTGYAMDYWGQGTTVTV
SSAWRHP

Sequence of entity 11 (K), FASTA

>1KB9_11 LIGHT CHAIN (VL) OF FV-FRAGMENT (chains K)
DIELTQTPVSLAASLGDRVTISCRASQDINNFLNWYQQKPDGTIKLLIYYTSRLHAGVPS
RFSGSGSGTDYSLTISNLEPEDIATYFCQHHIKFPWTFGAGTKLEIK

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	3
SMA	Stigmatellin a	C30 H42 O7	1
UQ6	5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy…	C39 H60 O4	1
PIE	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol	C43 H80 O13 P	1
PEF	Di-palmitoyl-3-sn-phosphatidylethanolamine	C37 H74 N O8 P	2
CDL	Cardiolipin	C81 H156 O17 P2	1
FES	FE2/S2 (inorganic) cluster	Fe2 S2	1
UMQ	Undecyl-maltoside	C23 H44 O11	1
PCF	1,2-diacyl-sn-glycero-3-phoshocholine	C40 H80 N O8 P	1

Primary citation

SPECIFIC ROLES OF PROTEIN-PHOSPHOLIPID INTERACTIONS IN THE YEAST CYTOCHROME BC1 COMPLEX STRUCTURE. Lange, C., Nett, J.H., Trumpower, B.L. et al. EMBO J (2001) 20:6591-6600. DOI 10.1093/emboj/20.23.6591 · 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
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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