8YIN: COR1 isoform 1
Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23694-bound state. Determined by electron microscopy at 2.74 Å resolution. Released 25 Dec 2024.
- Method
- Electron microscopy
- Resolution
- 2.74 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 20
- Atoms
- 32,364
- Mol. weight
- 460.35 kDa
- Ligands
- 8PE, A1D6O, UQ6, CN5
- Released
- 25 Dec 2024
Explore 8YIN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8YIN contains 218 α-helices and 124 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 L: 23 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 29-30 | 2 | 1 |
| β-strand | 34 | 1 | 2 |
| β-strand | 36 | 1 | 2 |
| β-strand | 37-41 | 5 | 1 |
| β-strand | 49-54 | 6 | 1 |
| α-helix | 59-61 | 3 | |
| α-helix | 71-74 | 4 | |
| α-helix | 80-87 | 8 | |
| β-strand | 92-97 | 6 | 1 |
| β-strand | 102-108 | 7 | 1 |
| α-helix | 115-123 | 9 | |
| α-helix | 134-154 | 21 | |
| α-helix | 156-167 | 12 | |
| α-helix | 190-195 | 6 | |
| α-helix | 197-200 | 4 | |
| β-strand | 207-211 | 5 | 1 |
| α-helix | 216-224 | 9 | |
| β-strand | 247-253 | 7 | 3 |
| β-strand | 259-266 | 8 | 3 |
| α-helix | 275-285 | 11 | |
| β-strand | 287-289 | 3 | 3 |
| α-helix | 293-296 | 4 | |
| α-helix | 306-309 | 4 | |
| β-strand | 314-321 | 8 | 3 |
| β-strand | 326-334 | 9 | 3 |
| α-helix | 340-351 | 12 | |
| α-helix | 353-356 | 4 | |
| α-helix | 360-377 | 18 | |
| α-helix | 385-388 | 4 | |
| α-helix | 389-391 | 3 | |
| α-helix | 393-396 | 4 | |
| α-helix | 400-402 | 3 | |
| α-helix | 403-410 | 8 | |
| α-helix | 415-425 | 11 | |
| β-strand | 432-437 | 6 | 3 |
| α-helix | 445-448 | 4 | |
| α-helix | 449-451 | 3 | |
Chains B and M: 17 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-19 | 2 | 7 |
| β-strand | 22 | 1 | 7 |
| β-strand | 28-35 | 8 | 7 |
| α-helix | 39-41 | 3 | |
| α-helix | 47-52 | 6 | |
| β-strand | 59 | 1 | 8 |
| α-helix | 64-72 | 9 | |
| β-strand | 76 | 1 | 7 |
| β-strand | 79-82 | 4 | 7 |
| β-strand | 87-94 | 8 | 7 |
| α-helix | 98-108 | 11 | |
| β-strand | 112 | 1 | 8 |
| 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 | 185-187 | 3 | 7 |
| β-strand | 190 | 1 | 7 |
| α-helix | 194-202 | 9 | |
| α-helix | 220-222 | 3 | |
| β-strand | 228-232 | 5 | 9 |
| β-strand | 237-245 | 9 | 9 |
| α-helix | 252-259 | 8 | |
| α-helix | 266-270 | 5 | |
| β-strand | 273-276 | 4 | 9 |
| β-strand | 283-291 | 9 | 9 |
| α-helix | 295-308 | 14 | |
| β-strand | 312-313 | 2 | 10 |
| α-helix | 319-328 | 10 | |
| α-helix | 340-342 | 3 | |
| β-strand | 345-346 | 2 | 10 |
| β-strand | 352-357 | 6 | 9 |
Chain C: 23 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 10-17 | 8 | |
| β-strand | 22-23 | 2 | 4 |
| α-helix | 28-31 | 4 | |
| α-helix | 32-50 | 19 | |
| α-helix | 61-70 | 10 | |
| α-helix | 75-84 | 10 | |
| α-helix | 86-100 | 15 | |
| α-helix | 112-132 | 21 | |
| β-strand | 137 | 1 | 5 |
| α-helix | 139-148 | 10 | |
| α-helix | 149-152 | 4 | |
| α-helix | 158-160 | 3 | |
| α-helix | 162-166 | 5 | |
| α-helix | 173-202 | 30 | |
| β-strand | 218-219 | 2 | 4 |
| α-helix | 229-239 | 11 | |
| α-helix | 254-257 | 4 | |
| β-strand | 259 | 1 | 5 |
| α-helix | 276-282 | 7 | |
| α-helix | 290-296 | 7 | |
| α-helix | 302-304 | 3 | |
| β-strand | 313 | 1 | 6 |
| α-helix | 326-339 | 14 | |
| α-helix | 351-354 | 4 | |
| α-helix | 358-361 | 4 | |
| α-helix | 362-366 | 5 | |
| α-helix | 367-377 | 11 | |
Chains D and O: 14 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 69-71 | 3 | |
| α-helix | 87-96 | 10 | |
| α-helix | 97-101 | 5 | |
| β-strand | 106 | 1 | 11 |
| β-strand | 111 | 1 | 12 |
| α-helix | 112-114 | 3 | |
| β-strand | 116 | 1 | 13 |
| β-strand | 120 | 1 | 13 |
| α-helix | 122-126 | 5 | |
| β-strand | 133-135 | 3 | 14 |
| β-strand | 146-148 | 3 | 14 |
| β-strand | 154 | 1 | 12 |
| α-helix | 163-166 | 4 | |
| β-strand | 176 | 1 | 11 |
| α-helix | 187-189 | 3 | |
| α-helix | 190-193 | 4 | |
| β-strand | 213-214 | 2 | 15 |
| β-strand | 222-223 | 2 | 15 |
| α-helix | 225-227 | 3 | |
| α-helix | 244-259 | 16 | |
| α-helix | 263-269 | 7 | |
| α-helix | 273-291 | 19 | |
| α-helix | 295-297 | 3 | |
| β-strand | 299-302 | 4 | 3 |
| α-helix | 304-306 | 3 | |
Chains E and P: 8 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-38 | 3 | |
| β-strand | 43 | 1 | 16 |
| α-helix | 51-62 | 12 | |
| α-helix | 66-69 | 4 | |
| α-helix | 72-80 | 9 | |
| β-strand | 96-97 | 2 | 17 |
| β-strand | 107-109 | 3 | 18 |
| α-helix | 111-113 | 3 | |
| β-strand | 116-120 | 5 | 18 |
| α-helix | 121-122 | 2 | |
| α-helix | 143-146 | 4 | |
| β-strand | 152-156 | 5 | 18 |
| α-helix | 166 | 1 | |
| β-strand | 167-168 | 2 | 19 |
| β-strand | 170 | 1 | 19 |
| β-strand | 176-177 | 2 | 19 |
| β-strand | 185 | 1 | 19 |
| β-strand | 191 | 1 | 19 |
| β-strand | 205-207 | 3 | 17 |
| β-strand | 211-214 | 4 | 17 |
Chain F: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 79-84 | 6 | |
| α-helix | 85-87 | 3 | |
| α-helix | 96-100 | 5 | |
| α-helix | 104-107 | 4 | |
| α-helix | 124-137 | 14 | |
| α-helix | 139-141 | 3 | |
Chains G and R: 8 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-17 | 13 | |
| α-helix | 21-23 | 3 | |
| α-helix | 25-34 | 10 | |
| α-helix | 45-47 | 3 | |
| β-strand | 49 | 1 | 6 |
| α-helix | 58-61 | 4 | |
| α-helix | 65-83 | 19 | |
| α-helix | 104-112 | 9 | |
| α-helix | 114-117 | 4 | |
Chains H and S: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-29 | 8 | 3 |
| β-strand | 34 | 1 | 16 |
| α-helix | 43-47 | 5 | |
| α-helix | 48-54 | 7 | |
| α-helix | 60-66 | 7 | |
| α-helix | 68-72 | 5 | |
6 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, L | protein | 431 | Saccharomyces cerevisiae | P07256 (AlphaFold model) |
| Cytochrome b | C, N | protein | 385 | Saccharomyces cerevisiae | P00163 (AlphaFold model) |
| Cytochrome b-c1 complex subunit 2, mitochondrial | B, M | protein | 352 | Saccharomyces cerevisiae | P07257 (AlphaFold model) |
| Cytochrome c1, heme protein, mitochondrial | D, O | protein | 248 | Saccharomyces cerevisiae | P07143 (AlphaFold model) |
| Cytochrome b-c1 complex subunit Rieske, mitochondrial | E, P | protein | 185 | Saccharomyces cerevisiae | P08067 |
| Cytochrome b-c1 complex subunit 8 | H, S | protein | 93 | Saccharomyces cerevisiae | P08525 |
| QCR6 isoform 1 | F, Q | protein | 75 | Saccharomyces cerevisiae | P00127 |
| Cytochrome b-c1 complex subunit 7 | G, R | protein | 126 | Saccharomyces cerevisiae | P00128 |
| Cytochrome b-c1 complex subunit 9, mitochondrial | I, T | protein | 55 | Saccharomyces cerevisiae | P22289 |
| Cytochrome b-c1 complex subunit 10, mitochondrial | U, V | protein | 52 | Saccharomyces cerevisiae | P37299 |
Sequence of entity 1 (A, L), FASTA
>8YIN_1 COR1 isoform 1 (chains A, L)
AEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVA
AKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLK
QVQDFEENDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNA
VVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVE
GEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSG
LWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVND
ANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYM
RIRSDMSMMRW
Sequence of entity 2 (C, N), FASTA
>8YIN_2 Cytochrome b (chains C, N)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK
Sequence of entity 3 (B, M), FASTA
>8YIN_3 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B, M)
LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGG
TFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ
CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEAD
LKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL
ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSP
AINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL
Sequence of entity 4 (D, O), FASTA
>8YIN_4 Cytochrome c1, heme protein, mitochondrial (chains D, O)
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHT
NEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIV
KARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTP
ATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV
FNPPKPRK
Sequence of entity 5 (E, P), FASTA
>8YIN_5 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains E, P)
KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLA
MAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDP
QWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGD
KVIVG
Sequence of entity 6 (H, S), FASTA
>8YIN_6 Cytochrome b-c1 complex subunit 8 (chains H, S)
GPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLI
PAGIYWYWWKNGNEYNEFLYSKAGREELERVNV
Sequence of entity 7 (F, Q), FASTA
>8YIN_7 QCR6 isoform 1 (chains F, Q)
EVTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEEFFHLQH
YLDTATAPRLFDKLK
Sequence of entity 8 (G, R), FASTA
>8YIN_8 Cytochrome b-c1 complex subunit 7 (chains G, R)
PQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALR
RLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELD
NIEVSK
Sequence of entity 9 (I, T), FASTA
>8YIN_9 Cytochrome b-c1 complex subunit 9, mitochondrial (chains I, T)
SSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAA
Sequence of entity 10 (U, V), FASTA
>8YIN_10 Cytochrome b-c1 complex subunit 10, mitochondrial (chains U, V)
KTGLHFGRLSLRSLTAYAPNLMLWGGASMLGLFVFTEGWPKFQDTLYKKIPL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 8PE | (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl… | C37 H74 N O8 P | 2 |
| A1D6O | 1-[2-[(4,6-dimethyl-1,3-benzothiazol-2-yl)sulfanylmethyl]-3-methyl-phenyl]-4-me… | C19 H19 N5 O S2 | 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 |
| 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 |
| CN3 | (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(prop… | C36 H68 O17 P2 | 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
- 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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