8YIO | pdb_00008yio

Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in azoxystrobin-bound state

PDB DOI: https://doi.org/10.2210/pdb8YIO/pdb
EM Map EMD-39324: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2024-02-29 Released: 2025-03-05
Deposition Author(s): Ye, Y., Li, Z.W., Yang, G.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.35 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in azoxystrobin-bound state

Ye, Y., Li, Z.W., Yang, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 460.36 kDa
Atom Count: 32,370
Modeled Residue Count: 3,992
Deposited Residue Count: 4,004
Unique protein chains: 10

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COR1 isoform 1	A, K [auth L]	431	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07256 Go to UniProtKB: P07256
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07256
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	B [auth C], E [auth N]	385	Saccharomyces cerevisiae	Mutation(s): 0 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00163 Go to UniProtKB: P00163
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00163
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 2, mitochondrial	C [auth B], L [auth M]	352	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07257 Go to UniProtKB: P07257
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07257
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	D, M [auth O]	248	Saccharomyces cerevisiae	Mutation(s): 0 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07143 Go to UniProtKB: P07143
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07143
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	F [auth E], N [auth P]	185	Saccharomyces cerevisiae	Mutation(s): 0 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08067 Go to UniProtKB: P08067
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08067
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
QCR6 isoform 1	G [auth F], O [auth Q]	75	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00127 Go to UniProtKB: P00127
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00127
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	H [auth G], P [auth R]	126	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00128 Go to UniProtKB: P00128
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00128
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 8	I [auth H], Q [auth S]	93	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P08525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08525 Go to UniProtKB: P08525
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08525
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 9, mitochondrial	J [auth I], R [auth T]	55	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22289 Go to UniProtKB: P22289
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22289
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 10, mitochondrial	S [auth U], T [auth V]	52	Saccharomyces cerevisiae	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P37299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P37299 Go to UniProtKB: P37299
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37299
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Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CN3 Query on CN3 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FA [auth N] MOL2 format, chain AA [auth C] MOL2 format, chain FA [auth N] mmCIF format, chain AA [auth C] mmCIF format, chain FA [auth N]	AA [auth C], FA [auth N]	(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate C₃₆ H₆₈ O₁₇ P₂ FMNZIMGRZPIVKW-XWHIBYANSA-N		Interactions Focus chain AA [auth C] Focus chain FA [auth N] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth N]
8PE Query on 8PE Download Ideal Coordinates CCD File SDF format, chain JA [auth N] SDF format, chain W [auth C] MOL2 format, chain JA [auth N] MOL2 format, chain W [auth C] mmCIF format, chain JA [auth N] mmCIF format, chain W [auth C]	JA [auth N], W [auth C]	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate C₃₇ H₇₄ N O₈ P RFJQNULIDFTTLL-PGUFJCEWSA-N		Interactions Focus chain JA [auth N] Focus chain W [auth C] Interactions & Density Focus chain JA [auth N] Focus chain W [auth C]
CN5 Query on CN5 Download Ideal Coordinates CCD File SDF format, chain Z [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain Z [auth C]	Z [auth C]	(5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate C₂₆ H₅₂ O₁₃ P₂ UKWPDXFRXMWSMQ-VWLOTQADSA-N		Interactions Focus chain Z [auth C] Interactions & Density Focus chain Z [auth C]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain IA [auth N] SDF format, chain MA [auth O] SDF format, chain Y [auth C] SDF format, chain HA [auth N] SDF format, chain CA [auth D] SDF format, chain BA [auth C] MOL2 format, chain IA [auth N] MOL2 format, chain MA [auth O] MOL2 format, chain Y [auth C] MOL2 format, chain HA [auth N] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth C] mmCIF format, chain IA [auth N] mmCIF format, chain MA [auth O] mmCIF format, chain Y [auth C] mmCIF format, chain HA [auth N] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth D] HA [auth N] IA [auth N] MA [auth O] BA [auth C], CA [auth D], HA [auth N], IA [auth N], MA [auth O], Y [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth C] Focus chain CA [auth D] Focus chain HA [auth N] Focus chain IA [auth N] Focus chain MA [auth O] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth D] Focus chain HA [auth N] Focus chain IA [auth N] Focus chain MA [auth O] Focus chain Y [auth C]
9PE Query on 9PE Download Ideal Coordinates CCD File SDF format, chain GA [auth N] SDF format, chain X [auth C] MOL2 format, chain GA [auth N] MOL2 format, chain X [auth C] mmCIF format, chain GA [auth N] mmCIF format, chain X [auth C]	GA [auth N], X [auth C]	(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate C₃₀ H₆₀ N O₈ P RWBMCOYSJCETON-MUUNZHRXSA-N		Interactions Focus chain GA [auth N] Focus chain X [auth C] Interactions & Density Focus chain GA [auth N] Focus chain X [auth C]
UQ6 Query on UQ6 Download Ideal Coordinates CCD File SDF format, chain KA [auth N] SDF format, chain V [auth C] MOL2 format, chain KA [auth N] MOL2 format, chain V [auth C] mmCIF format, chain KA [auth N] mmCIF format, chain V [auth C]	KA [auth N], V [auth C]	5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL C₃₉ H₆₀ O₄ DYOSCPIQEYRQEO-XQCASOQKSA-N		Interactions Focus chain KA [auth N] Focus chain V [auth C] Interactions & Density Focus chain KA [auth N] Focus chain V [auth C]
6PH Query on 6PH Download Ideal Coordinates CCD File SDF format, chain LA [auth O] SDF format, chain EA [auth N] MOL2 format, chain LA [auth O] MOL2 format, chain EA [auth N] mmCIF format, chain LA [auth O] mmCIF format, chain EA [auth N]	EA [auth N], LA [auth O]	(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate C₃₁ H₆₁ O₈ P UOOPRMYYAWVCCZ-GDLZYMKVSA-N		Interactions Focus chain EA [auth N] Focus chain LA [auth O] Interactions & Density Focus chain EA [auth N] Focus chain LA [auth O]
AZO (Subject of Investigation/LOI) Query on AZO Download Ideal Coordinates CCD File SDF format, chain DA [auth N] SDF format, chain U [auth C] MOL2 format, chain DA [auth N] MOL2 format, chain U [auth C] mmCIF format, chain DA [auth N] mmCIF format, chain U [auth C]	DA [auth N], U [auth C]	METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE C₂₂ H₁₇ N₃ O₅ WFDXOXNFNRHQEC-GHRIWEEISA-N		Interactions Focus chain DA [auth N] Focus chain U [auth C] Interactions & Density Focus chain DA [auth N] Focus chain U [auth C]