8YHQ: COR1 isoform 1
Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in pyraclostrobin-bound state. Determined by electron microscopy at 2.42 Å resolution. Released 25 Dec 2024.
- Method
- Electron microscopy
- Resolution
- 2.42 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 20
- Atoms
- 32,385
- Mol. weight
- 460.62 kDa
- Ligands
- CN3, 7PH, A1D6K, UQ6
- Released
- 25 Dec 2024
Explore 8YHQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8YHQ contains 236 α-helices and 105 β-strands across 20 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.
Chains A and J: 24 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 | 59-61 | 3 | |
| α-helix | 69-77 | 9 | |
| α-helix | 80-87 | 8 | |
| β-strand | 92-97 | 6 | 1 |
| β-strand | 102-108 | 7 | 1 |
| α-helix | 110-112 | 3 | |
| α-helix | 113-120 | 8 | |
| α-helix | 121-126 | 6 | |
| α-helix | 134-154 | 21 | |
| α-helix | 156-168 | 13 | |
| α-helix | 173-175 | 3 | |
| α-helix | 190-200 | 11 | |
| α-helix | 203-205 | 3 | |
| β-strand | 206-212 | 7 | 1 |
| α-helix | 216-225 | 10 | |
| α-helix | 235-238 | 4 | |
| α-helix | 241-242 | 2 | |
| β-strand | 247-253 | 7 | 2 |
| β-strand | 259-266 | 8 | 2 |
| α-helix | 275-285 | 11 | |
| β-strand | 287-289 | 3 | 2 |
| α-helix | 294-297 | 4 | |
| α-helix | 303-306 | 4 | |
| β-strand | 314-321 | 8 | 2 |
| β-strand | 326-334 | 9 | 2 |
| α-helix | 340-356 | 17 | |
| α-helix | 360-377 | 18 | |
| α-helix | 383-397 | 15 | |
| α-helix | 403-410 | 8 | |
| α-helix | 415-425 | 11 | |
| β-strand | 432-437 | 6 | 2 |
| α-helix | 445-449 | 5 | |
| α-helix | 450-452 | 3 | |
Chains B and K: 21 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-22 | 5 | 5 |
| β-strand | 28-35 | 8 | 5 |
| α-helix | 39-41 | 3 | |
| α-helix | 47-54 | 8 | |
| β-strand | 59 | 1 | 6 |
| α-helix | 64-74 | 11 | |
| β-strand | 76-82 | 7 | 5 |
| β-strand | 87-94 | 8 | 5 |
| α-helix | 98-110 | 13 | |
| β-strand | 112 | 1 | 6 |
| 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 | 5 |
| α-helix | 194-202 | 9 | |
| α-helix | 205-207 | 3 | |
| α-helix | 220-222 | 3 | |
| β-strand | 228-232 | 5 | 7 |
| β-strand | 237-245 | 9 | 7 |
| α-helix | 247-249 | 3 | |
| α-helix | 250-261 | 12 | |
| β-strand | 273-279 | 7 | 7 |
| β-strand | 282-291 | 10 | 7 |
| α-helix | 294-308 | 15 | |
| β-strand | 312-313 | 2 | 8 |
| α-helix | 315-317 | 3 | |
| α-helix | 318-328 | 11 | |
| α-helix | 340-342 | 3 | |
| β-strand | 345-346 | 2 | 8 |
| β-strand | 352-357 | 6 | 7 |
| α-helix | 359-361 | 3 | |
| α-helix | 365-367 | 3 | |
Chains C and L: 24 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 | 3 |
| α-helix | 28-31 | 4 | |
| α-helix | 32-51 | 20 | |
| α-helix | 61-70 | 10 | |
| α-helix | 75-103 | 29 | |
| α-helix | 111-135 | 25 | |
| β-strand | 137 | 1 | 4 |
| 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 | 3 |
| α-helix | 226-246 | 21 | |
| α-helix | 254-257 | 4 | |
| β-strand | 259 | 1 | 4 |
| α-helix | 260 | 1 | |
| 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 | 321-339 | 19 | |
| α-helix | 348-361 | 14 | |
| α-helix | 362-366 | 5 | |
| α-helix | 367-382 | 16 | |
Chains D and M: 17 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-67 | 4 | |
| α-helix | 69-71 | 3 | |
| α-helix | 87-96 | 10 | |
| α-helix | 97-101 | 5 | |
| β-strand | 111 | 1 | 9 |
| α-helix | 112-115 | 4 | |
| β-strand | 116 | 1 | 10 |
| β-strand | 120 | 1 | 10 |
| α-helix | 122-129 | 8 | |
| β-strand | 133-135 | 3 | 11 |
| α-helix | 136-138 | 3 | |
| 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 | 188-195 | 8 | |
| α-helix | 202-203 | 2 | |
| α-helix | 208-209 | 2 | |
| β-strand | 213-214 | 2 | 12 |
| β-strand | 222-223 | 2 | 12 |
| α-helix | 225-227 | 3 | |
| α-helix | 244-259 | 16 | |
| α-helix | 263-291 | 29 | |
| α-helix | 293-297 | 5 | |
| β-strand | 299-302 | 4 | 2 |
Chain E: 4 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 43 | 1 | 13 |
| α-helix | 49-80 | 32 | |
| α-helix | 86-90 | 5 | |
| β-strand | 108-111 | 4 | 14 |
| β-strand | 114-120 | 7 | 14 |
| α-helix | 143-146 | 4 | |
| β-strand | 152-156 | 5 | 14 |
| β-strand | 167 | 1 | 15 |
| β-strand | 177 | 1 | 15 |
| β-strand | 185 | 1 | 16 |
| β-strand | 191 | 1 | 16 |
| α-helix | 201-203 | 3 | |
| β-strand | 207 | 1 | 17 |
| β-strand | 212 | 1 | 17 |
Chain F: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 77-84 | 8 | |
| α-helix | 85-87 | 3 | |
| α-helix | 90-93 | 4 | |
| α-helix | 95-99 | 5 | |
| α-helix | 124-138 | 15 | |
| α-helix | 139-141 | 3 | |
Chain G: 11 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-17 | 13 | |
| α-helix | 19-36 | 18 | |
| α-helix | 39-41 | 3 | |
| α-helix | 45-47 | 3 | |
| α-helix | 54-61 | 8 | |
| α-helix | 65-83 | 19 | |
| α-helix | 90-92 | 3 | |
| α-helix | 94-95 | 2 | |
| α-helix | 96-98 | 3 | |
| α-helix | 104-120 | 17 | |
| β-strand | 123 | 1 | 20 |
| α-helix | 124-126 | 3 | |
Chains H and Q: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-29 | 8 | 2 |
| α-helix | 31-33 | 3 | |
| β-strand | 34 | 1 | 13 |
| α-helix | 47-54 | 8 | |
| α-helix | 57-80 | 24 | |
| α-helix | 86-92 | 7 | |
7 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 |
|---|
| COR1 isoform 1 | A, J | protein | 431 | Saccharomyces cerevisiae | P07256 (AlphaFold model) |
| Cytochrome b | C, L | protein | 385 | Saccharomyces cerevisiae | P00163 (AlphaFold model) |
| Cytochrome b-c1 complex subunit 2, mitochondrial | B, K | protein | 352 | Saccharomyces cerevisiae | P07257 (AlphaFold model) |
| quinol--cytochrome-c reductase | D, M | protein | 248 | Saccharomyces cerevisiae | P07143 (AlphaFold model) |
| Cytochrome b-c1 complex subunit Rieske, mitochondrial | E, N | protein | 185 | Saccharomyces cerevisiae | P08067 |
| QCR6 isoform 1 | F, O | protein | 75 | Saccharomyces cerevisiae | P00127 |
| Cytochrome b-c1 complex subunit 7 | G, P | protein | 126 | Saccharomyces cerevisiae | P00128 |
| Cytochrome b-c1 complex subunit 8 | H, Q | protein | 93 | Saccharomyces cerevisiae | P08525 |
| Cytochrome b-c1 complex subunit 9, mitochondrial | I, R | protein | 55 | Saccharomyces cerevisiae | P22289 |
| Cytochrome b-c1 complex subunit 10, mitochondrial | S, T | protein | 52 | Saccharomyces cerevisiae | P37299 |
Sequence of entity 1 (A, J), FASTA
>8YHQ_1 COR1 isoform 1 (chains A, J)
AEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVA
AKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLK
QVQDFEENDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNA
VVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVE
GEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSG
LWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVND
ANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYM
RIRSDMSMMRW
Sequence of entity 2 (C, L), FASTA
>8YHQ_2 Cytochrome b (chains C, L)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK
Sequence of entity 3 (B, K), FASTA
>8YHQ_3 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B, K)
LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGG
TFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ
CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEAD
LKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL
ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSP
AINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL
Sequence of entity 4 (D, M), FASTA
>8YHQ_4 quinol--cytochrome-c reductase (chains D, M)
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHT
NEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIV
KARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTP
ATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV
FNPPKPRK
Sequence of entity 5 (E, N), FASTA
>8YHQ_5 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains E, N)
KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLA
MAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDP
QWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGD
KVIVG
Sequence of entity 6 (F, O), FASTA
>8YHQ_6 QCR6 isoform 1 (chains F, O)
EVTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEEFFHLQH
YLDTATAPRLFDKLK
Sequence of entity 7 (G, P), FASTA
>8YHQ_7 Cytochrome b-c1 complex subunit 7 (chains G, P)
PQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALR
RLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELD
NIEVSK
Sequence of entity 8 (H, Q), FASTA
>8YHQ_8 Cytochrome b-c1 complex subunit 8 (chains H, Q)
GPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLI
PAGIYWYWWKNGNEYNEFLYSKAGREELERVNV
Sequence of entity 9 (I, R), FASTA
>8YHQ_9 Cytochrome b-c1 complex subunit 9, mitochondrial (chains I, R)
SSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAA
Sequence of entity 10 (S, T), FASTA
>8YHQ_10 Cytochrome b-c1 complex subunit 10, mitochondrial (chains S, T)
KTGLHFGRLSLRSLTAYAPNLMLWGGASMLGLFVFTEGWPKFQDTLYKKIPL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CN3 | (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(prop… | C36 H68 O17 P2 | 1 |
| 7PH | (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate | C29 H57 O8 P | 2 |
| A1D6K | methyl ~{N}-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]phenyl]-~{N}-methoxy-… | C19 H18 Cl N3 O4 | 2 |
| UQ6 | 5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy… | C39 H60 O4 | 2 |
| CN5 | (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-dipho… | C26 H52 O13 P2 | 1 |
| 8PE | (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl… | C37 H74 N O8 P | 2 |
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 6 |
| 9PE | (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]et… | C30 H60 N O8 P | 2 |
| 6PH | (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate | C31 H61 O8 P | 2 |
Primary citation
Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome bc 1 Complex Enabling Rational Design of Inhibitors. Wang, Y.X., Ye, Y., Li, Z.W. et al. J Am Chem Soc (2024) 146:33903-33913. DOI 10.1021/jacs.4c12595 · 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
- 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
Browse structure collections
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