4PD4: Cytochrome b-c1 complex subunit 1, mitochondrial
Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action. Determined by X-ray diffraction at 3.04 Å resolution. Released 11 Jun 2014.
- Method
- X-ray diffraction
- Resolution
- 3.04 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Mus musculus
- Chains
- 11
- Atoms
- 17,646
- Mol. weight
- 251.15 kDa
- Ligands
- UMQ, 3PH, HEM, AOQ
- Released
- 11 Jun 2014
Explore 4PD4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4PD4 contains 103 α-helices and 85 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: 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 | 69-76 | 8 | |
| α-helix | 80-88 | 9 | |
| β-strand | 92-97 | 6 | 1 |
| β-strand | 102-108 | 7 | 1 |
| α-helix | 114-121 | 8 | |
| α-helix | 122-126 | 5 | |
| α-helix | 137-140 | 4 | |
| α-helix | 144-147 | 4 | |
| α-helix | 151-154 | 4 | |
| α-helix | 156-168 | 13 | |
| α-helix | 173-175 | 3 | |
| α-helix | 190-200 | 11 | |
| β-strand | 206-212 | 7 | 1 |
| α-helix | 216-223 | 8 | |
| α-helix | 234-236 | 3 | |
| 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 | 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 | 383-396 | 14 | |
| α-helix | 403-412 | 10 | |
| α-helix | 415-425 | 11 | |
| β-strand | 431-437 | 7 | 2 |
| α-helix | 445-448 | 4 | |
| α-helix | 449-452 | 4 | |
Chain B: 22 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-19 | 2 | 3 |
| β-strand | 22 | 1 | 4 |
| β-strand | 28-30 | 3 | 5 |
| β-strand | 33-35 | 3 | 3 |
| β-strand | 36 | 1 | 6 |
| α-helix | 39-41 | 3 | |
| α-helix | 47-52 | 6 | |
| β-strand | 59 | 1 | 7 |
| α-helix | 64-74 | 11 | |
| β-strand | 77-78 | 2 | 5 |
| β-strand | 81-82 | 2 | 8 |
| β-strand | 86 | 1 | 6 |
| β-strand | 87-88 | 2 | 8 |
| β-strand | 91-94 | 4 | 5 |
| α-helix | 95-97 | 3 | |
| α-helix | 98-111 | 14 | |
| β-strand | 112 | 1 | 7 |
| α-helix | 116-118 | 3 | |
| α-helix | 119-123 | 5 | |
| α-helix | 124-134 | 11 | |
| α-helix | 138-149 | 12 | |
| α-helix | 170-179 | 10 | |
| α-helix | 182-184 | 3 | |
| β-strand | 185-187 | 3 | 3 |
| β-strand | 190 | 1 | 4 |
| α-helix | 194-203 | 10 | |
| α-helix | 205-208 | 4 | |
| α-helix | 220-222 | 3 | |
| β-strand | 228-232 | 5 | 9 |
| β-strand | 237-242 | 6 | 9 |
| α-helix | 250-260 | 11 | |
| α-helix | 266-269 | 4 | |
| β-strand | 273-278 | 6 | 9 |
| β-strand | 283-291 | 9 | 9 |
| α-helix | 294-299 | 6 | |
| α-helix | 304-310 | 7 | |
| β-strand | 312-313 | 2 | 10 |
| α-helix | 315-317 | 3 | |
| α-helix | 320-326 | 7 | |
| β-strand | 345-346 | 2 | 10 |
| β-strand | 352-357 | 6 | 9 |
| α-helix | 359-361 | 3 | |
| α-helix | 365-367 | 3 | |
Chain C: 20 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 10-14 | 5 | |
| β-strand | 21-23 | 3 | 11 |
| α-helix | 31-51 | 21 | |
| α-helix | 58-70 | 13 | |
| α-helix | 75-102 | 28 | |
| α-helix | 111-133 | 23 | |
| α-helix | 138-149 | 12 | |
| α-helix | 158-164 | 7 | |
| α-helix | 173-202 | 30 | |
| β-strand | 218-220 | 3 | 11 |
| α-helix | 224-246 | 23 | |
| α-helix | 254-257 | 4 | |
| α-helix | 276-283 | 8 | |
| α-helix | 288-300 | 13 | |
| α-helix | 301-303 | 3 | |
| α-helix | 305-308 | 4 | |
| α-helix | 316-318 | 3 | |
| α-helix | 320-341 | 22 | |
| α-helix | 348-361 | 14 | |
| α-helix | 362-366 | 5 | |
| α-helix | 367-380 | 14 | |
Chain D: 11 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-67 | 4 | |
| α-helix | 87-99 | 13 | |
| α-helix | 101-103 | 3 | |
| β-strand | 111 | 1 | 12 |
| α-helix | 112-115 | 4 | |
| β-strand | 116 | 1 | 13 |
| β-strand | 120 | 1 | 13 |
| α-helix | 122-130 | 9 | |
| β-strand | 154 | 1 | 12 |
| α-helix | 162-167 | 6 | |
| α-helix | 174-176 | 3 | |
| α-helix | 188-195 | 8 | |
| β-strand | 213-214 | 2 | 14 |
| β-strand | 222-223 | 2 | 14 |
| α-helix | 226-227 | 2 | |
| α-helix | 247-259 | 13 | |
| α-helix | 263-296 | 34 | |
| β-strand | 299 | 1 | 2 |
| β-strand | 302 | 1 | 15 |
Chain E: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-38 | 3 | |
| α-helix | 44-45 | 2 | |
| α-helix | 51-80 | 30 | |
| α-helix | 84-85 | 2 | |
| β-strand | 95-97 | 3 | 16 |
| β-strand | 106-111 | 6 | 17 |
| β-strand | 114-120 | 7 | 17 |
| α-helix | 123-129 | 7 | |
| α-helix | 143-146 | 4 | |
| β-strand | 152-156 | 5 | 17 |
| α-helix | 166 | 1 | |
| β-strand | 167-170 | 4 | 18 |
| β-strand | 174-178 | 5 | 18 |
| β-strand | 183-186 | 4 | 18 |
| β-strand | 191 | 1 | 18 |
| β-strand | 206-208 | 3 | 16 |
| β-strand | 211-213 | 3 | 16 |
Chain F: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 79-86 | 8 | |
| α-helix | 89-110 | 22 | |
| α-helix | 114-116 | 3 | |
| α-helix | 124-138 | 15 | |
| α-helix | 142-145 | 4 | |
Chain G: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-17 | 13 | |
| α-helix | 19-35 | 17 | |
| α-helix | 38-41 | 4 | |
| α-helix | 45-48 | 4 | |
| α-helix | 54-58 | 5 | |
| α-helix | 65-84 | 20 | |
| α-helix | 104-122 | 19 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| β-strand | 24 | 1 | 15 |
| β-strand | 26-29 | 4 | 2 |
| α-helix | 50-79 | 30 | |
| α-helix | 83-85 | 3 | |
| 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 |
|---|
| Cytochrome b-c1 complex subunit 1, mitochondrial | A | protein | 431 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P07256 (AlphaFold model) |
| Cytochrome b-c1 complex subunit 2, mitochondrial | B | protein | 352 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P07257 (AlphaFold model) |
| Cytochrome b | C | protein | 385 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P00163 (AlphaFold model) |
| Cytochrome c1, heme protein, mitochondrial | D | protein | 248 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P07143 (AlphaFold model) |
| Cytochrome b-c1 complex subunit Rieske, mitochondrial | E | protein | 185 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P08067 |
| Cytochrome b-c1 complex subunit 6 | F | protein | 74 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P00127 |
| Cytochrome b-c1 complex subunit 7 | G | protein | 126 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P00128 |
| Cytochrome b-c1 complex subunit 8 | H | protein | 93 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P08525 |
| Cytochrome b-c1 complex subunit 9 | I | protein | 57 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P22289 |
| Igh protein | J | protein | 127 | Mus musculus | Q53VQ5 |
| Ig kappa chain V-V region HP 124E1 | K | protein | 107 | Mus musculus | P01647 |
Sequence of entity 1 (A), FASTA
>4PD4_1 Cytochrome b-c1 complex subunit 1, mitochondrial (chains A)
AEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVA
AKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLK
QVQDFEDNDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNA
VVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVE
GEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSG
LWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVND
ANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYM
RIRSDMSMMRW
Sequence of entity 2 (B), FASTA
>4PD4_2 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B)
LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGG
TFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ
CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEAD
LKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL
ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSP
AINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL
Sequence of entity 3 (C), FASTA
>4PD4_3 Cytochrome b (chains C)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK
Sequence of entity 4 (D), FASTA
>4PD4_4 Cytochrome c1, heme protein, mitochondrial (chains D)
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHT
NEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIV
KARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTP
ATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV
FNPPKPRK
Sequence of entity 5 (E), FASTA
>4PD4_5 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains E)
KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLA
MAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDP
QWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGD
KVIVG
Sequence of entity 6 (F), FASTA
>4PD4_6 Cytochrome b-c1 complex subunit 6 (chains F)
VTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEEFFHLQHY
LDTATAPRLFDKLK
Sequence of entity 7 (G), FASTA
>4PD4_7 Cytochrome b-c1 complex subunit 7 (chains G)
PQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALR
RLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELD
NIEVSK
Sequence of entity 8 (H), FASTA
>4PD4_8 Cytochrome b-c1 complex subunit 8 (chains H)
GPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLI
PAGIYWYWWKNGNEYNEFLYSKAGREELERVNV
Sequence of entity 9 (I), FASTA
>4PD4_9 Cytochrome b-c1 complex subunit 9 (chains I)
SFSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAA
Sequence of entity 10 (J), FASTA
>4PD4_10 Igh protein (chains J)
EVKLQESGAGLVQPSQSLSLTCSVTGYSITSGYYWNWIRLFPGNKLEWVGYISNVGDNNY
NPSLKDRLSITRDTSKNQFFLKLNSVTTEDTATYYCARSEYYSVTGYAMDYWGQGTTVTV
SSAWRHP
Sequence of entity 11 (K), FASTA
>4PD4_11 Ig kappa chain V-V region HP 124E1 (chains K)
DIELTQTPVSLAASLGDRVTISCRASQDINNFLNWYQQKPDGTIKLLIYYTSRLHAGVPS
RFSGSGSGTDYSLTISNLEPEDIATYFCQHHIKFPWTFGAGTKLEIK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| UMQ | Undecyl-maltoside | C23 H44 O11 | 1 |
| 3PH | 1,2-diacyl-glycerol-3-sn-phosphate | C39 H77 O8 P | 3 |
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 3 |
| AOQ | 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione | C22 H19 Cl O3 | 1 |
| 3PE | 1,2-Distearoyl-sn-glycerophosphoethanolamine | C41 H82 N O8 P | 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 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 1 |
Primary citation
Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action. Birth, D., Kao, W.C., Hunte, C. Nat Commun (2014) 5:4029-4029. DOI 10.1038/ncomms5029 · 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
Browse structure collections
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