1P84: HDBT inhibited Yeast Cytochrome bc1 Complex

HDBT inhibited Yeast Cytochrome bc1 Complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 29 Jul 2003.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Saccharomyces cerevisiae, Mus musculus
Chains: 11
Atoms: 18,069
Mol. weight: 252.74 kDa
Ligands: FES, CDL, PC1, 3PE
Released: 29 Jul 2003

Explore 1P84 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1P84 contains 116 α-helices and 79 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: 20 helices, 12 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	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
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	293-296	4
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	403-411	9
α-helix	415-425	11
β-strand	432-437	6	2
α-helix	445-450	6

Chain B: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	18-20	3	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	98-111	14
β-strand	112	1	4
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
β-strand	185-190	6	3
α-helix	194-203	10
α-helix	206-208	3
α-helix	220-221	2
β-strand	228-232	5	5
β-strand	237-245	9	5
α-helix	250-260	11
α-helix	266-270	5
β-strand	273-278	6	5
β-strand	283-291	9	5
α-helix	294-309	16
α-helix	316-318	3
α-helix	320-323	4
β-strand	352-357	6	5
α-helix	359-361	3

Chain C: 24 helices, 4 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	6
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	7
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	6
α-helix	221-225	5
α-helix	226-241	16
α-helix	242-246	5
α-helix	254-257	4
β-strand	259	1	7
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: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	64-67	4
α-helix	69-72	4
α-helix	87-99	13
α-helix	101-103	3
β-strand	111	1	8
α-helix	112-115	4
β-strand	116	1	9
β-strand	120	1	9
α-helix	122-130	9
β-strand	133-135	3	10
β-strand	146-148	3	10
β-strand	154	1	8
α-helix	155-157	3
α-helix	162-167	6
α-helix	174-176	3
α-helix	187-195	9
α-helix	202-203	2
α-helix	208-209	2
β-strand	213-214	2	11
β-strand	222-223	2	11
α-helix	244-259	16
α-helix	263-296	34
β-strand	299-302	4	2

Chain E: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
β-strand	43	1	12
α-helix	52-79	28
α-helix	80-82	3
α-helix	84-85	2
α-helix	86-88	3
β-strand	94-97	4	13
α-helix	98-100	3
β-strand	106-111	6	14
β-strand	114-120	7	14
α-helix	123-130	8
α-helix	134-136	3
α-helix	143-146	4
β-strand	152-156	5	14
α-helix	166	1
β-strand	167-170	4	15
β-strand	175-178	4	15
β-strand	183-185	3	15
β-strand	191-193	3	15
α-helix	199-201	3
β-strand	205-208	4	13
β-strand	211-214	4	13

Chain F: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	77-86	10
α-helix	89-110	22
α-helix	124-138	15
α-helix	142-145	4

Chain G: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	5-17	13
α-helix	19-22	4
α-helix	26-36	11
α-helix	38-41	4
α-helix	45-48	4
α-helix	54-62	9
α-helix	65-84	20
α-helix	90-92	3
α-helix	94-95	2
α-helix	104-121	18

Chain H: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
α-helix	19-21	3
β-strand	24-29	6	2
α-helix	31-33	3
β-strand	34	1	12
α-helix	35-36	2
α-helix	50-52	3
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 kDa protein	F	protein	74	Saccharomyces cerevisiae	P00127
Ubiquinol-cytochrome C reductase complex 14 kDa 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 kDa 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

>1P84_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

>1P84_2 Ubiquinol-cytochrome C reductase complex core protein 2 (chains B)
LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGG
TFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ
CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEAD
LKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL
ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSP
AINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL

Sequence of entity 3 (C), FASTA

>1P84_3 cytochrome b (chains C)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FTLTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK

Sequence of entity 4 (D), FASTA

>1P84_4 Cytochrome c1, heme protein (chains D)
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHT
NEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIV
KARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTP
ATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV
FNPPKP

Sequence of entity 5 (E), FASTA

>1P84_5 Ubiquinol-cytochrome C reductase iron-sulfur subunit (chains E)
KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLA
MAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDP
QWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGD
KVIVG

Sequence of entity 6 (F), FASTA

>1P84_6 Ubiquinol-cytochrome C reductase complex 17 kDa protein (chains F)
VTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEEFFHLQHY
LDTATAPRLFDKLK

Sequence of entity 7 (G), FASTA

>1P84_7 Ubiquinol-cytochrome C reductase complex 14 kDa protein (chains G)
QSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALRR
LPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELDN
IEVSK

Sequence of entity 8 (H), FASTA

>1P84_8 Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C (chains H)
GPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLI
PAGIYWYWWKNGNEYNEFLYSKAGREELERVNV

Sequence of entity 9 (I), FASTA

>1P84_9 Ubiquinol-cytochrome C reductase complex 7.3 kDa protein (chains I)
SSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAA

Sequence of entity 10 (J), FASTA

>1P84_10 Heavy Chain (Vh) Of Fv-Fragment (chains J)
EVKLQESGAGLVQPSQSLSLTCSVTGYSITSGYYWNWIRLFPGNKLEWVGYISNVGDNNY
NPSLKDRLSITRDTSKNQFFLKLNSVTTEDTATYYCARSEYYSVTGYAMDYWGQGTTVTV
SSAWRHP

Sequence of entity 11 (K), FASTA

>1P84_11 Light Chain (Vl) Of Fv-Fragment (chains K)
DIELTQTPVSLAASLGDRVTISCRASQDINNFLNWYQQKPDGTIKLLIYYTSRLHAGVPS
RFSGSGSGTDYSLTISNLEPEDIATYFCQHHIKFPWTFGAGTKLEIK

Ligands and cofactors

ID	Name	Formula	Copies
FES	FE2/S2 (inorganic) cluster	Fe2 S2	1
CDL	Cardiolipin	C81 H156 O17 P2	1
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	1
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	2
UQ6	5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy…	C39 H60 O4	1
DBT	5-heptyl-6-hydroxy-1,3-benzothiazole-4,7-dione	C14 H17 N O3 S	1
HEC	Heme C	C34 H36 Fe N4 O4	3
UMQ	Undecyl-maltoside	C23 H44 O11	1
3PH	1,2-diacyl-glycerol-3-sn-phosphate	C39 H77 O8 P	2

Primary citation

Structure of the yeast cytochrome bc1 complex with a hydroxyquinone anion Qo site inhibitor bound. Palsdottir, H., Lojero, C.G., Trumpower, B.L. et al. J Biol Chem (2003) 278:31303-31311. DOI 10.1074/jbc.M302195200 · 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
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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