8IOG

Cryo-EM structure of porcine bc1 complex in isolated state

PDB DOI: https://doi.org/10.2210/pdb8IOG/pdb
EM Map EMD-35618: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Sus scrofa
Expression System: Sus scrofa
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2023-03-11 Released: 2024-04-17
Deposition Author(s): Wang, Y.X., Dong, J.Q., Yang, G.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.88 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of porcine bc1 complex in isolated state

Wang, Y.X., Dong, J.Q., Yang, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 523 kDa
Atom Count: 33,413
Modelled Residue Count: 4,181
Deposited Residue Count: 4,632
Unique protein chains: 11

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	A, L [auth a]	379	Sus scrofa	Mutation(s): 1 Gene Names: MT-CYB, COB, CYTB, MTCYB Membrane Entity: Yes
UniProt
Find proteins for P24964 (Sus scrofa) Explore P24964 Go to UniProtKB: P24964
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24964
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	B, M [auth b]	326	Sus scrofa	Mutation(s): 0 Gene Names: LOC100525869 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1UNI7 (Sus scrofa) Explore A0A4X1UNI7 Go to UniProtKB: A0A4X1UNI7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1UNI7
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	C, N [auth c]	196	Sus scrofa	Mutation(s): 0 Gene Names: LOC100522678 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1TWD8 (Sus scrofa) Explore A0A4X1TWD8 Go to UniProtKB: A0A4X1TWD8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1TWD8
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 1, mitochondrial	D, O [auth d]	480	Sus scrofa	Mutation(s): 0 Gene Names: LOC100156879
UniProt
Find proteins for A0A8D0PK14 (Sus scrofa) Explore A0A8D0PK14 Go to UniProtKB: A0A8D0PK14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8D0PK14
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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 2, mitochondrial	E, P [auth e]	453	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1V0F2 (Sus scrofa) Explore A0A4X1V0F2 Go to UniProtKB: A0A4X1V0F2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1V0F2
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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 6	F, Q [auth f]	91	Sus scrofa	Mutation(s): 0 Gene Names: UQCRH, LOC100524873 Membrane Entity: Yes
UniProt
Find proteins for F1S3W0 (Sus scrofa) Explore F1S3W0 Go to UniProtKB: F1S3W0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F1S3W0
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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	G, R [auth g]	111	Sus scrofa	Mutation(s): 0 Gene Names: UQCRB Membrane Entity: Yes
UniProt
Find proteins for A0A4X1U2M7 (Sus scrofa) Explore A0A4X1U2M7 Go to UniProtKB: A0A4X1U2M7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1U2M7
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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	H, S [auth h]	82	Sus scrofa	Mutation(s): 0 Gene Names: UQCRQ, LOC100524308 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1UYT9 (Sus scrofa) Explore A0A4X1UYT9 Go to UniProtKB: A0A4X1UYT9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1UYT9
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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, T [auth i]	64	Sus scrofa	Mutation(s): 0 Gene Names: UQCR10 Membrane Entity: Yes
UniProt
Find proteins for Q2EN79 (Sus scrofa) Explore Q2EN79 Go to UniProtKB: Q2EN79
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2EN79
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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	J, U [auth j]	56	Sus scrofa	Mutation(s): 0 Gene Names: LOC100524239 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1VTU3 (Sus scrofa) Explore A0A4X1VTU3 Go to UniProtKB: A0A4X1VTU3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VTU3
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	K, V [auth k]	78	Sus scrofa	Mutation(s): 0 Gene Names: LOC100522678 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1TWD8 (Sus scrofa) Explore A0A4X1TWD8 Go to UniProtKB: A0A4X1TWD8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1TWD8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain GA [auth a] SDF format, chain BA [auth D] MOL2 format, chain GA [auth a] MOL2 format, chain BA [auth D]	BA [auth D], GA [auth a]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BA [auth D] Focus chain GA [auth a] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth a]
PEE Query on PEE Download Ideal Coordinates CCD File SDF format, chain FA [auth a] SDF format, chain Y [auth A] SDF format, chain CA [auth D] MOL2 format, chain FA [auth a] MOL2 format, chain Y [auth A] MOL2 format, chain CA [auth D]	CA [auth D], FA [auth a], Y [auth A]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain CA [auth D] Focus chain FA [auth a] Focus chain Y [auth A] Interactions & Density Focus chain CA [auth D] Focus chain FA [auth a] Focus chain Y [auth A]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain HA [auth b] MOL2 format, chain Z [auth B] MOL2 format, chain HA [auth b]	HA [auth b], Z [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain HA [auth b] Focus chain Z [auth B] Interactions & Density Focus chain HA [auth b] Focus chain Z [auth B]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain EA [auth a] SDF format, chain DA [auth a] SDF format, chain W [auth A] SDF format, chain X [auth A] MOL2 format, chain EA [auth a] MOL2 format, chain DA [auth a] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A]	DA [auth a], EA [auth a], W [auth A], X [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain DA [auth a] Focus chain EA [auth a] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain DA [auth a] Focus chain EA [auth a] Focus chain W [auth A] Focus chain X [auth A]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain IA [auth c] MOL2 format, chain AA [auth C] MOL2 format, chain IA [auth c]	AA [auth C], IA [auth c]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain IA [auth c] Interactions & Density Focus chain AA [auth C] Focus chain IA [auth c]