8ZNO | pdb_00008zno

Cryo-EM structure of Arachis hypogaea bc1 complex

PDB DOI: https://doi.org/10.2210/pdb8ZNO/pdb
EM Map EMD-60275: EMDB EMDataResource

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

Deposited: 2024-05-27 Released: 2025-06-04
Deposition Author(s): Ye, Y., Dong, J.Q., Yang, G.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.02 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 Arachis hypogaea bc1 complex

Ye, Y., Dong, J.Q., Yang, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 496.5 kDa
Atom Count: 34,447
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
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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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| 3D Structure

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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain UA [auth P] SDF format, chain QA [auth O] SDF format, chain NA [auth O] SDF format, chain LA [auth N] SDF format, chain FA [auth D] SDF format, chain DA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth P] MOL2 format, chain QA [auth O] MOL2 format, chain NA [auth O] MOL2 format, chain LA [auth N] MOL2 format, chain FA [auth D] MOL2 format, chain DA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth P] mmCIF format, chain QA [auth O] mmCIF format, chain NA [auth O] mmCIF format, chain LA [auth N] mmCIF format, chain FA [auth D] mmCIF format, chain DA [auth C]	DA [auth C] FA [auth D] LA [auth N] NA [auth O] QA [auth O] DA [auth C], FA [auth D], LA [auth N], NA [auth O], QA [auth O], UA [auth P], V [auth B]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain DA [auth C] Focus chain FA [auth D] Focus chain LA [auth N] Focus chain NA [auth O] Focus chain QA [auth O] Focus chain UA [auth P] Focus chain V [auth B] Interactions & Density Focus chain DA [auth C] Focus chain FA [auth D] Focus chain LA [auth N] Focus chain NA [auth O] Focus chain QA [auth O] Focus chain UA [auth P] Focus chain V [auth B]
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain RA [auth P] MOL2 format, chain RA [auth P] mmCIF format, chain RA [auth P]	RA [auth P]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain RA [auth P] Interactions & Density Focus chain RA [auth P]
3PE (Subject of Investigation/LOI) Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain XA [auth S] SDF format, chain X [auth C] SDF format, chain WA [auth R] SDF format, chain W [auth C] SDF format, chain SA [auth P] SDF format, chain MA [auth O] SDF format, chain JA [auth G] SDF format, chain IA [auth E] SDF format, chain EA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain XA [auth S] MOL2 format, chain X [auth C] MOL2 format, chain WA [auth R] MOL2 format, chain W [auth C] MOL2 format, chain SA [auth P] MOL2 format, chain MA [auth O] MOL2 format, chain JA [auth G] MOL2 format, chain IA [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain XA [auth S] mmCIF format, chain X [auth C] mmCIF format, chain WA [auth R] mmCIF format, chain W [auth C] mmCIF format, chain SA [auth P] mmCIF format, chain MA [auth O] mmCIF format, chain JA [auth G] mmCIF format, chain IA [auth E] mmCIF format, chain EA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] EA [auth C] IA [auth E] AA [auth C], BA [auth C], CA [auth C], EA [auth C], IA [auth E], JA [auth G], MA [auth O], SA [auth P], W [auth C], WA [auth R], X [auth C], XA [auth S]	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 EA [auth C] Focus chain IA [auth E] Focus chain JA [auth G] Focus chain MA [auth O] Focus chain SA [auth P] Focus chain W [auth C] Focus chain WA [auth R] Focus chain X [auth C] Focus chain XA [auth S] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain EA [auth C] Focus chain IA [auth E] Focus chain JA [auth G] Focus chain MA [auth O] Focus chain SA [auth P] Focus chain W [auth C] Focus chain WA [auth R] Focus chain X [auth C] Focus chain XA [auth S]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain TA [auth P] SDF format, chain GA [auth D] MOL2 format, chain TA [auth P] MOL2 format, chain GA [auth D] mmCIF format, chain TA [auth P] mmCIF format, chain GA [auth D]	GA [auth D], TA [auth P]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain GA [auth D] Focus chain TA [auth P] Interactions & Density Focus chain GA [auth D] Focus chain TA [auth P]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain PA [auth O] SDF format, chain OA [auth O] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain PA [auth O] MOL2 format, chain OA [auth O] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain PA [auth O] mmCIF format, chain OA [auth O]	OA [auth O], PA [auth O], Y [auth C], Z [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 Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain OA [auth O] Focus chain PA [auth O] Focus chain Y [auth C] Focus chain Z [auth C]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain VA [auth Q] SDF format, chain HA [auth E] MOL2 format, chain VA [auth Q] MOL2 format, chain HA [auth E] mmCIF format, chain VA [auth Q] mmCIF format, chain HA [auth E]	HA [auth E], VA [auth Q]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain HA [auth E] Focus chain VA [auth Q] Interactions & Density Focus chain HA [auth E] Focus chain VA [auth Q]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain KA [auth N] MOL2 format, chain U [auth B] MOL2 format, chain KA [auth N] mmCIF format, chain U [auth B] mmCIF format, chain KA [auth N]	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]