8ZOM | pdb_00008zom

Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex

PDB DOI: https://doi.org/10.2210/pdb8ZOM/pdb
EM Map EMD-60307: EMDB EMDataResource

Classification: PLANT PROTEIN
Organism(s): Arachis hypogaea
Mutation(s): No

Deposited: 2024-05-28 Released: 2025-06-04
Deposition Author(s): Cui, G.R., Wang, Y.X., Yang, G.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex

Cui, G.R., Wang, Y.X., Yang, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 495.82 kDa
Atom Count: 34,466
Modeled Residue Count: 4,221
Deposited Residue Count: 4,222
Unique protein chains: 10

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial-processing peptidase subunit alpha	A, K [auth M]	460	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for A0A445DY18 (Arachis hypogaea) Explore A0A445DY18 Go to UniProtKB: A0A445DY18
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A445DY18
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial-processing peptidase subunit beta	B, L [auth N]	487	Arachis hypogaea	Mutation(s): 0 EC: 3.4.24.64
UniProt
Find proteins for A0A445CDV5 (Arachis hypogaea) Explore A0A445CDV5 Go to UniProtKB: A0A445CDV5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A445CDV5
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	C, M [auth O]	386	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for A0A8F2YUY6 (Arachis hypogaea) Explore A0A8F2YUY6 Go to UniProtKB: A0A8F2YUY6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8F2YUY6
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c domain-containing protein	D, N [auth P]	242	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for A0A445EV57 (Arachis hypogaea) Explore A0A445EV57 Go to UniProtKB: A0A445EV57
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A445EV57
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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	E, O [auth Q]	196	Arachis hypogaea	Mutation(s): 0 EC: 7.1.1.8
UniProt
Find proteins for A0A444YS04 (Arachis hypogaea) Explore A0A444YS04 Go to UniProtKB: A0A444YS04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A444YS04
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	F, P [auth R]	117	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for A0A445CVZ9 (Arachis hypogaea) Explore A0A445CVZ9 Go to UniProtKB: A0A445CVZ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A445CVZ9
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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 8	G, Q [auth S]	70	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for A0A445EVJ9 (Arachis hypogaea) Explore A0A445EVJ9 Go to UniProtKB: A0A445EVJ9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A445EVJ9
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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 6	H, R [auth T]	64	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for A0A444WZ62 (Arachis hypogaea) Explore A0A444WZ62 Go to UniProtKB: A0A444WZ62
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A444WZ62
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Complex III subunit 9	I [auth J], S [auth V]	60	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for A0A445CQN5 (Arachis hypogaea) Explore A0A445CQN5 Go to UniProtKB: A0A445CQN5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A445CQN5
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Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome c reductase complex 6.7 kDa protein	J [auth K], T [auth W]	29	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for A0A0A6ZDN8 (Arachis hypogaea) Explore A0A0A6ZDN8 Go to UniProtKB: A0A0A6ZDN8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0A6ZDN8
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Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain LA [auth N] SDF format, chain MA [auth N] SDF format, chain QA [auth O] SDF format, chain TA [auth O] SDF format, chain V [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain LA [auth N] MOL2 format, chain MA [auth N] MOL2 format, chain QA [auth O] MOL2 format, chain TA [auth O] MOL2 format, chain V [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain LA [auth N] mmCIF format, chain MA [auth N] mmCIF format, chain QA [auth O] mmCIF format, chain TA [auth O] mmCIF format, chain V [auth B]	FA [auth C] LA [auth N] MA [auth N] QA [auth O] TA [auth O] FA [auth C], LA [auth N], MA [auth N], QA [auth O], TA [auth O], V [auth B]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain FA [auth C] Focus chain LA [auth N] Focus chain MA [auth N] Focus chain QA [auth O] Focus chain TA [auth O] Focus chain V [auth B] Interactions & Density Focus chain FA [auth C] Focus chain LA [auth N] Focus chain MA [auth N] Focus chain QA [auth O] Focus chain TA [auth O] Focus chain V [auth B]
PC1 (Subject of Investigation/LOI) Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain WA [auth Q] MOL2 format, chain WA [auth Q] mmCIF format, chain WA [auth Q]	WA [auth Q]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain WA [auth Q] Interactions & Density Focus chain WA [auth Q]
3PE (Subject of Investigation/LOI) Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain EA [auth C] SDF format, chain GA [auth C] SDF format, chain JA [auth K] SDF format, chain RA [auth O] SDF format, chain SA [auth O] SDF format, chain XA [auth R] SDF format, chain YA [auth R] SDF format, chain Z [auth C] SDF format, chain DA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain JA [auth K] MOL2 format, chain RA [auth O] MOL2 format, chain SA [auth O] MOL2 format, chain XA [auth R] MOL2 format, chain YA [auth R] MOL2 format, chain Z [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain JA [auth K] mmCIF format, chain RA [auth O] mmCIF format, chain SA [auth O] mmCIF format, chain XA [auth R] mmCIF format, chain YA [auth R] mmCIF format, chain Z [auth C] mmCIF format, chain DA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], GA [auth C], JA [auth K], RA [auth O], SA [auth O], XA [auth R], YA [auth R], Z [auth C]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain GA [auth C] Focus chain JA [auth K] Focus chain RA [auth O] Focus chain SA [auth O] Focus chain XA [auth R] Focus chain YA [auth R] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain GA [auth C] Focus chain JA [auth K] Focus chain RA [auth O] Focus chain SA [auth O] Focus chain XA [auth R] Focus chain YA [auth R] Focus chain Z [auth C]
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain UA [auth P] MOL2 format, chain HA [auth D] MOL2 format, chain UA [auth P] mmCIF format, chain HA [auth D] mmCIF format, chain UA [auth P]	HA [auth D], UA [auth P]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain HA [auth D] Focus chain UA [auth P] Interactions & Density Focus chain HA [auth D] Focus chain UA [auth P]
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain OA [auth O] SDF format, chain PA [auth O] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain OA [auth O] MOL2 format, chain PA [auth O] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain OA [auth O] mmCIF format, chain PA [auth O] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	OA [auth O], PA [auth O], X [auth C], Y [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain OA [auth O] Focus chain PA [auth O] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain OA [auth O] Focus chain PA [auth O] Focus chain X [auth C] Focus chain Y [auth C]
A1D6K Query on A1D6K Download:Ideal Coordinates CCD File SDF format, chain NA [auth O] SDF format, chain W [auth C] MOL2 format, chain NA [auth O] MOL2 format, chain W [auth C] mmCIF format, chain NA [auth O] mmCIF format, chain W [auth C]	NA [auth O], W [auth C]	methyl ~{N}-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]phenyl]-~{N}-methoxy-carbamate C₁₉ H₁₈ Cl N₃ O₄ HZRSNVGNWUDEFX-UHFFFAOYSA-N		Interactions Focus chain NA [auth O] Focus chain W [auth C] Interactions & Density Focus chain NA [auth O] Focus chain W [auth C]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain IA [auth E] SDF format, chain VA [auth Q] MOL2 format, chain IA [auth E] MOL2 format, chain VA [auth Q] mmCIF format, chain IA [auth E] mmCIF format, chain VA [auth Q]	IA [auth E], VA [auth Q]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain IA [auth E] Focus chain VA [auth Q] Interactions & Density Focus chain IA [auth E] Focus chain VA [auth Q]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain KA [auth N] SDF format, chain U [auth B] MOL2 format, chain KA [auth N] MOL2 format, chain U [auth B] mmCIF format, chain KA [auth N] mmCIF format, chain U [auth B]	KA [auth N], U [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain KA [auth N] Focus chain U [auth B] Interactions & Density Focus chain KA [auth N] Focus chain U [auth B]