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 | Sheet |
|---|
| 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 | Sheet |
|---|
| 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
Browse structure collections
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