7QHM | pdb_00007qhm

Cytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV2) from Corynebacterium glutamicum (stigmatellin and azide bound)

PDB DOI: https://doi.org/10.2210/pdb7QHM/pdb
EM Map EMD-13976: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Corynebacterium glutamicum ATCC 13032
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-12-13 Released: 2022-05-18
Deposition Author(s): Kao, W.-C., Hunte, C.
Funding Organization(s): German Research Foundation (DFG), French Infrastructure for Integrated Structural Biology (FRISBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 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

Structural basis for safe and efficient energy conversion in a respiratory supercomplex.

Kao, W.C., Ortmann de Percin Northumberland, C., Cheng, T.C., Ortiz, J., Durand, A., von Loeffelholz, O., Schilling, O., Biniossek, M.L., Klaholz, B.P., Hunte, C.

(2022) Nat Commun 13: 545-545

PubMed: 35087070 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-28179-x
Primary Citation Related Structures:
7QHM, 7QHO

PubMed Abstract:
Proton-translocating respiratory complexes assemble into supercomplexes that are proposed to increase the efficiency of energy conversion and limit the production of harmful reactive oxygen species during aerobic cellular respiration. Cytochrome bc complexes and cytochrome aa ₃ oxidases are major drivers of the proton motive force that fuels ATP generation via respiration, but how wasteful electron- and proton transfer is controlled to enhance safety and efficiency in the context of supercomplexes is not known. Here, we address this question with the 2.8 Å resolution cryo-EM structure of the cytochrome bcc-aa ₃ (III ₂-IV ₂) supercomplex from the actinobacterium Corynebacterium glutamicum. Menaquinone, substrate mimics, lycopene, an unexpected Q _c site, dioxygen, proton transfer routes, and conformational states of key protonable residues are resolved. Our results show how safe and efficient energy conversion is achieved in a respiratory supercomplex through controlled electron and proton transfer. The structure may guide the rational design of drugs against actinobacteria that cause diphtheria and tuberculosis.

Organizational Affiliation

Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. wei-chun.kao@biochemie.uni-freiburg.de.

Macromolecule Content

Total Structure Weight: 774.24 kDa
Atom Count: 49,530
Modeled Residue Count: 5,886
Deposited Residue Count: 6,462
Unique protein chains: 13

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bc1 complex Rieske iron-sulfur subunit	A, N	408	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: qcrA, Cgl2190, cg2404 Membrane Entity: Yes
UniProt
Find proteins for Q79VE8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q79VE8 Go to UniProtKB: Q79VE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q79VE8
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bc1 complex cytochrome b subunit	B, O	539	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: qcrB, Cgl2189, cg2403 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for Q79VE9 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q79VE9 Go to UniProtKB: Q79VE9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q79VE9
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome bc1 complex cytochrome c subunit	C, P	283	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: qcrC, Cgl2191, cg2405 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for Q8NNK5 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NNK5 Go to UniProtKB: Q8NNK5
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NNK5
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	D, Q	594	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: ctaD, Cgl2523, cg2780 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for Q79VD7 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q79VD7 Go to UniProtKB: Q79VD7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q79VD7
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	E, R	331	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: ctaC, Cgl2195, cg2409 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for Q8NNK2 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NNK2 Go to UniProtKB: Q8NNK2
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NNK2
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	F, S	205	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: ctaE, Cgl2192, cg2406 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for Q9AEL8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q9AEL8 Go to UniProtKB: Q9AEL8
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9AEL8
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide 4	G, T	143	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: ctaF, Cgl2194, cg2408 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for Q8NNK3 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NNK3 Go to UniProtKB: Q8NNK3
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NNK3
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Cgl2664/cg2949	H, U	163	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: Cgl2664, cg2949 Membrane Entity: Yes
UniProt
Find proteins for Q8NMB4 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NMB4 Go to UniProtKB: Q8NMB4
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NMB4
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized membrane protein Cgl2017/cg2211	I, V	147	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: Cgl2017, cg2211 Membrane Entity: Yes
UniProt
Find proteins for Q8NP09 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NP09 Go to UniProtKB: Q8NP09
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UniProt Group	Q8NP09
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical membrane protein	J, W	112	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: Cgl0373 Membrane Entity: Yes
UniProt
Find proteins for Q8NTD4 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NTD4 Go to UniProtKB: Q8NTD4
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UniProt Group	Q8NTD4
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Actinobacterial supercomplex, subunit C (AscC)	K, X	73	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: Cgl0818
UniProt
Find proteins for Q8NS61 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NS61 Go to UniProtKB: Q8NS61
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UniProt Group	Q8NS61
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical membrane protein	L, Y	65	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: Cgl0673 Membrane Entity: Yes
UniProt
Find proteins for Q8NSJ8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NSJ8 Go to UniProtKB: Q8NSJ8
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UniProt Group	Q8NSJ8
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine biosynthesis protein X	M, Z	168	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: thiX, Cgl2332, cg2561 Membrane Entity: Yes
UniProt
Find proteins for P42461 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore P42461 Go to UniProtKB: P42461
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42461
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Reference Sequence

Small Molecules

Ligands 21 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IZL (Subject of Investigation/LOI) Query on IZL Download:Ideal Coordinates CCD File SDF format, chain UB [auth N] SDF format, chain BA [auth A] MOL2 format, chain UB [auth N] MOL2 format, chain BA [auth A] mmCIF format, chain UB [auth N] mmCIF format, chain BA [auth A]	BA [auth A], UB [auth N]	[(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate C₇₄ H₁₃₃ O₃₉ P RFJQNGLGKTXNKA-YXJCWACHSA-N		Interactions Focus chain BA [auth A] Focus chain UB [auth N] Interactions & Density Focus chain BA [auth A] Focus chain UB [auth N]
CDL (Subject of Investigation/LOI) Query on CDL Download:Ideal Coordinates CCD File SDF format, chain ZC [auth T] SDF format, chain ZA [auth D] SDF format, chain YA [auth D] SDF format, chain WC [auth T] SDF format, chain VC [auth S] SDF format, chain NC [auth Q] SDF format, chain NA [auth B] SDF format, chain MC [auth Q] SDF format, chain MB [auth I] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain HB [auth G] SDF format, chain GD [auth V] SDF format, chain GB [auth G] SDF format, chain FB [auth F] SDF format, chain BC [auth O] MOL2 format, chain ZC [auth T] MOL2 format, chain ZA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain WC [auth T] MOL2 format, chain VC [auth S] MOL2 format, chain NC [auth Q] MOL2 format, chain NA [auth B] MOL2 format, chain MC [auth Q] MOL2 format, chain MB [auth I] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain HB [auth G] MOL2 format, chain GD [auth V] MOL2 format, chain GB [auth G] MOL2 format, chain FB [auth F] MOL2 format, chain BC [auth O] mmCIF format, chain ZC [auth T] mmCIF format, chain ZA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain WC [auth T] mmCIF format, chain VC [auth S] mmCIF format, chain NC [auth Q] mmCIF format, chain NA [auth B] mmCIF format, chain MC [auth Q] mmCIF format, chain MB [auth I] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain HB [auth G] mmCIF format, chain GD [auth V] mmCIF format, chain GB [auth G] mmCIF format, chain FB [auth F] mmCIF format, chain BC [auth O]	BC [auth O] FB [auth F] GB [auth G] GD [auth V] HB [auth G] BC [auth O], FB [auth F], GB [auth G], GD [auth V], HB [auth G], JA [auth B], KA [auth B], MB [auth I], MC [auth Q], NA [auth B], NC [auth Q], VC [auth S], WC [auth T], YA [auth D], ZA [auth D], ZC [auth T]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BC [auth O] Focus chain FB [auth F] Focus chain GB [auth G] Focus chain GD [auth V] Focus chain HB [auth G] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain MB [auth I] Focus chain MC [auth Q] Focus chain NA [auth B] Focus chain NC [auth Q] Focus chain VC [auth S] Focus chain WC [auth T] Focus chain YA [auth D] Focus chain ZA [auth D] Focus chain ZC [auth T] Interactions & Density Focus chain BC [auth O] Focus chain FB [auth F] Focus chain GB [auth G] Focus chain GD [auth V] Focus chain HB [auth G] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain MB [auth I] Focus chain MC [auth Q] Focus chain NA [auth B] Focus chain NC [auth Q] Focus chain VC [auth S] Focus chain WC [auth T] Focus chain YA [auth D] Focus chain ZA [auth D] Focus chain ZC [auth T]
IX7 (Subject of Investigation/LOI) Query on IX7 Download:Ideal Coordinates CCD File SDF format, chain LB [auth H] SDF format, chain FD [auth U] MOL2 format, chain LB [auth H] MOL2 format, chain FD [auth U] mmCIF format, chain LB [auth H] mmCIF format, chain FD [auth U]	FD [auth U], LB [auth H]	[(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{S})-10-methylhenicosanoate C₇₀ H₁₃₁ O₂₄ P JKZXDYNAHQQSJQ-SDJDXWPFSA-N		Interactions Focus chain FD [auth U] Focus chain LB [auth H] Interactions & Density Focus chain FD [auth U] Focus chain LB [auth H]
HAS (Subject of Investigation/LOI) Query on HAS Download:Ideal Coordinates CCD File SDF format, chain TA [auth D] SDF format, chain SA [auth D] SDF format, chain HC [auth Q] SDF format, chain GC [auth Q] MOL2 format, chain TA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain HC [auth Q] MOL2 format, chain GC [auth Q] mmCIF format, chain TA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain HC [auth Q] mmCIF format, chain GC [auth Q]	GC [auth Q], HC [auth Q], SA [auth D], TA [auth D]	HEME-AS C₅₄ H₆₄ Fe N₄ O₆ PDYODZVCODUKFH-ZOMLSHGTSA-L		Interactions Focus chain GC [auth Q] Focus chain HC [auth Q] Focus chain SA [auth D] Focus chain TA [auth D] Interactions & Density Focus chain GC [auth Q] Focus chain HC [auth Q] Focus chain SA [auth D] Focus chain TA [auth D]
9YF (Subject of Investigation/LOI) Query on 9YF Download:Ideal Coordinates CCD File SDF format, chain VB [auth N] SDF format, chain KB [auth H] SDF format, chain ED [auth U] SDF format, chain CA [auth A] MOL2 format, chain VB [auth N] MOL2 format, chain KB [auth H] MOL2 format, chain ED [auth U] MOL2 format, chain CA [auth A] mmCIF format, chain VB [auth N] mmCIF format, chain KB [auth H] mmCIF format, chain ED [auth U] mmCIF format, chain CA [auth A]	CA [auth A], ED [auth U], KB [auth H], VB [auth N]	(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate C₄₄ H₈₅ O₁₃ P GRDWPDVMAXODDM-LZYRCPELSA-N		Interactions Focus chain CA [auth A] Focus chain ED [auth U] Focus chain KB [auth H] Focus chain VB [auth N] Interactions & Density Focus chain CA [auth A] Focus chain ED [auth U] Focus chain KB [auth H] Focus chain VB [auth N]
MQ9 (Subject of Investigation/LOI) Query on MQ9 Download:Ideal Coordinates CCD File SDF format, chain RB [auth N] SDF format, chain IA [auth B] SDF format, chain DA [auth A] SDF format, chain AC [auth O] MOL2 format, chain RB [auth N] MOL2 format, chain IA [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain AC [auth O] mmCIF format, chain RB [auth N] mmCIF format, chain IA [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain AC [auth O]	AC [auth O], DA [auth A], IA [auth B], RB [auth N]	MENAQUINONE-9 C₅₆ H₈₀ O₂ WCRXHNIUHQUASO-ABFXHILCSA-N		Interactions Focus chain AC [auth O] Focus chain DA [auth A] Focus chain IA [auth B] Focus chain RB [auth N] Interactions & Density Focus chain AC [auth O] Focus chain DA [auth A] Focus chain IA [auth B] Focus chain RB [auth N]
3PE (Subject of Investigation/LOI) Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain YC [auth T] SDF format, chain XC [auth T] SDF format, chain UC [auth S] SDF format, chain TC [auth R] SDF format, chain SB [auth N] SDF format, chain RA [auth C] SDF format, chain QA [auth C] SDF format, chain OC [auth Q] SDF format, chain OB [auth L] SDF format, chain NB [auth J] SDF format, chain HD [auth W] SDF format, chain FC [auth P] SDF format, chain EB [auth F] SDF format, chain EA [auth A] SDF format, chain BD [auth T] SDF format, chain AD [auth T] SDF format, chain AB [auth D] MOL2 format, chain YC [auth T] MOL2 format, chain XC [auth T] MOL2 format, chain UC [auth S] MOL2 format, chain TC [auth R] MOL2 format, chain SB [auth N] MOL2 format, chain RA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain OC [auth Q] MOL2 format, chain OB [auth L] MOL2 format, chain NB [auth J] MOL2 format, chain HD [auth W] MOL2 format, chain FC [auth P] MOL2 format, chain EB [auth F] MOL2 format, chain EA [auth A] MOL2 format, chain BD [auth T] MOL2 format, chain AD [auth T] MOL2 format, chain AB [auth D] mmCIF format, chain YC [auth T] mmCIF format, chain XC [auth T] mmCIF format, chain UC [auth S] mmCIF format, chain TC [auth R] mmCIF format, chain SB [auth N] mmCIF format, chain RA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain OC [auth Q] mmCIF format, chain OB [auth L] mmCIF format, chain NB [auth J] mmCIF format, chain HD [auth W] mmCIF format, chain FC [auth P] mmCIF format, chain EB [auth F] mmCIF format, chain EA [auth A] mmCIF format, chain BD [auth T] mmCIF format, chain AD [auth T] mmCIF format, chain AB [auth D]	AB [auth D] AD [auth T] BD [auth T] EA [auth A] EB [auth F] AB [auth D], AD [auth T], BD [auth T], EA [auth A], EB [auth F], FC [auth P], HD [auth W], NB [auth J], OB [auth L], OC [auth Q], QA [auth C], RA [auth C], SB [auth N], TC [auth R], UC [auth S], XC [auth T], YC [auth T]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain AB [auth D] Focus chain AD [auth T] Focus chain BD [auth T] Focus chain EA [auth A] Focus chain EB [auth F] Focus chain FC [auth P] Focus chain HD [auth W] Focus chain NB [auth J] Focus chain OB [auth L] Focus chain OC [auth Q] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SB [auth N] Focus chain TC [auth R] Focus chain UC [auth S] Focus chain XC [auth T] Focus chain YC [auth T] Interactions & Density Focus chain AB [auth D] Focus chain AD [auth T] Focus chain BD [auth T] Focus chain EA [auth A] Focus chain EB [auth F] Focus chain FC [auth P] Focus chain HD [auth W] Focus chain NB [auth J] Focus chain OB [auth L] Focus chain OC [auth Q] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SB [auth N] Focus chain TC [auth R] Focus chain UC [auth S] Focus chain XC [auth T] Focus chain YC [auth T]
DGA (Subject of Investigation/LOI) Query on DGA Download:Ideal Coordinates CCD File SDF format, chain SC [auth R] SDF format, chain PB [auth M] SDF format, chain ID [auth Z] SDF format, chain IB [auth H] SDF format, chain DB [auth E] SDF format, chain CD [auth U] MOL2 format, chain SC [auth R] MOL2 format, chain PB [auth M] MOL2 format, chain ID [auth Z] MOL2 format, chain IB [auth H] MOL2 format, chain DB [auth E] MOL2 format, chain CD [auth U] mmCIF format, chain SC [auth R] mmCIF format, chain PB [auth M] mmCIF format, chain ID [auth Z] mmCIF format, chain IB [auth H] mmCIF format, chain DB [auth E] mmCIF format, chain CD [auth U]	CD [auth U] DB [auth E] IB [auth H] ID [auth Z] PB [auth M] CD [auth U], DB [auth E], IB [auth H], ID [auth Z], PB [auth M], SC [auth R]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain CD [auth U] Focus chain DB [auth E] Focus chain IB [auth H] Focus chain ID [auth Z] Focus chain PB [auth M] Focus chain SC [auth R] Interactions & Density Focus chain CD [auth U] Focus chain DB [auth E] Focus chain IB [auth H] Focus chain ID [auth Z] Focus chain PB [auth M] Focus chain SC [auth R]
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain PA [auth C] SDF format, chain OA [auth C] SDF format, chain EC [auth P] SDF format, chain DC [auth P] MOL2 format, chain PA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain EC [auth P] MOL2 format, chain DC [auth P] mmCIF format, chain PA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain EC [auth P] mmCIF format, chain DC [auth P]	DC [auth P], EC [auth P], OA [auth C], PA [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain DC [auth P] Focus chain EC [auth P] Focus chain OA [auth C] Focus chain PA [auth C] Interactions & Density Focus chain DC [auth P] Focus chain EC [auth P] Focus chain OA [auth C] Focus chain PA [auth C]
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain ZB [auth O] SDF format, chain YB [auth O] SDF format, chain HA [auth B] SDF format, chain GA [auth B] MOL2 format, chain ZB [auth O] MOL2 format, chain YB [auth O] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain ZB [auth O] mmCIF format, chain YB [auth O] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B]	GA [auth B], HA [auth B], YB [auth O], ZB [auth O]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain YB [auth O] Focus chain ZB [auth O] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain YB [auth O] Focus chain ZB [auth O]
LYC (Subject of Investigation/LOI) Query on LYC Download:Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain CC [auth O] MOL2 format, chain LA [auth B] MOL2 format, chain CC [auth O] mmCIF format, chain LA [auth B] mmCIF format, chain CC [auth O]	CC [auth O], LA [auth B]	LYCOPENE C₄₀ H₅₆ OAIJSZIZWZSQBC-GYZMGTAESA-N		Interactions Focus chain CC [auth O] Focus chain LA [auth B] Interactions & Density Focus chain CC [auth O] Focus chain LA [auth B]
SMA (Subject of Investigation/LOI) Query on SMA Download:Ideal Coordinates CCD File SDF format, chain XB [auth O] SDF format, chain FA [auth B] MOL2 format, chain XB [auth O] MOL2 format, chain FA [auth B] mmCIF format, chain XB [auth O] mmCIF format, chain FA [auth B]	FA [auth B], XB [auth O]	STIGMATELLIN A C₃₀ H₄₂ O₇ UZHDGDDPOPDJGM-WPPYOTIYSA-N		Interactions Focus chain FA [auth B] Focus chain XB [auth O] Interactions & Density Focus chain FA [auth B] Focus chain XB [auth O]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain WB [auth O] SDF format, chain MA [auth B] MOL2 format, chain WB [auth O] MOL2 format, chain MA [auth B] mmCIF format, chain WB [auth O] mmCIF format, chain MA [auth B]	MA [auth B], WB [auth O]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain MA [auth B] Focus chain WB [auth O] Interactions & Density Focus chain MA [auth B] Focus chain WB [auth O]
PLM (Subject of Investigation/LOI) Query on PLM Download:Ideal Coordinates CCD File SDF format, chain QB [auth M] SDF format, chain JD [auth Z] SDF format, chain JB [auth H] SDF format, chain DD [auth U] MOL2 format, chain QB [auth M] MOL2 format, chain JD [auth Z] MOL2 format, chain JB [auth H] MOL2 format, chain DD [auth U] mmCIF format, chain QB [auth M] mmCIF format, chain JD [auth Z] mmCIF format, chain JB [auth H] mmCIF format, chain DD [auth U]	DD [auth U], JB [auth H], JD [auth Z], QB [auth M]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain DD [auth U] Focus chain JB [auth H] Focus chain JD [auth Z] Focus chain QB [auth M] Interactions & Density Focus chain DD [auth U] Focus chain JB [auth H] Focus chain JD [auth Z] Focus chain QB [auth M]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain TB [auth N] SDF format, chain AA [auth A] MOL2 format, chain TB [auth N] MOL2 format, chain AA [auth A] mmCIF format, chain TB [auth N] mmCIF format, chain AA [auth A]	AA [auth A], TB [auth N]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain TB [auth N] Interactions & Density Focus chain AA [auth A] Focus chain TB [auth N]
CUA (Subject of Investigation/LOI) Query on CUA Download:Ideal Coordinates CCD File SDF format, chain RC [auth R] SDF format, chain QC [auth R] SDF format, chain CB [auth E] SDF format, chain BB [auth E] MOL2 format, chain RC [auth R] MOL2 format, chain QC [auth R] MOL2 format, chain CB [auth E] MOL2 format, chain BB [auth E] mmCIF format, chain RC [auth R] mmCIF format, chain QC [auth R] mmCIF format, chain CB [auth E] mmCIF format, chain BB [auth E]	BB [auth E], CB [auth E], QC [auth R], RC [auth R]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain BB [auth E] Focus chain CB [auth E] Focus chain QC [auth R] Focus chain RC [auth R] Interactions & Density Focus chain BB [auth E] Focus chain CB [auth E] Focus chain QC [auth R] Focus chain RC [auth R]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain UA [auth D] SDF format, chain IC [auth Q] MOL2 format, chain UA [auth D] MOL2 format, chain IC [auth Q] mmCIF format, chain UA [auth D] mmCIF format, chain IC [auth Q]	IC [auth Q], UA [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain IC [auth Q] Focus chain UA [auth D] Interactions & Density Focus chain IC [auth Q] Focus chain UA [auth D]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain VA [auth D] SDF format, chain PC [auth R] MOL2 format, chain VA [auth D] MOL2 format, chain PC [auth R] mmCIF format, chain VA [auth D] mmCIF format, chain PC [auth R]	PC [auth R], VA [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain PC [auth R] Focus chain VA [auth D] Interactions & Density Focus chain PC [auth R] Focus chain VA [auth D]
AZI (Subject of Investigation/LOI) Query on AZI Download:Ideal Coordinates CCD File SDF format, chain XA [auth D] SDF format, chain KC [auth Q] MOL2 format, chain XA [auth D] MOL2 format, chain KC [auth Q] mmCIF format, chain XA [auth D] mmCIF format, chain KC [auth Q]	KC [auth Q], XA [auth D]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain KC [auth Q] Focus chain XA [auth D] Interactions & Density Focus chain KC [auth Q] Focus chain XA [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain WA [auth D] SDF format, chain JC [auth Q] MOL2 format, chain WA [auth D] MOL2 format, chain JC [auth Q] mmCIF format, chain WA [auth D] mmCIF format, chain JC [auth Q]	JC [auth Q], WA [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain JC [auth Q] Focus chain WA [auth D] Interactions & Density Focus chain JC [auth Q] Focus chain WA [auth D]
OXY (Subject of Investigation/LOI) Query on OXY Download:Ideal Coordinates CCD File SDF format, chain LC [auth Q] MOL2 format, chain LC [auth Q] mmCIF format, chain LC [auth Q]	LC [auth Q]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain LC [auth Q] Interactions & Density Focus chain LC [auth Q]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2
RECONSTRUCTION	cisTEM	1.0.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-18

Deposition Author(s):

Kao, W.-C.

Hunte, C.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	BIOSS EXC-294
German Research Foundation (DFG)	Germany	CIBSS EXC-2189 Project ID 390939984
German Research Foundation (DFG)	Germany	Project-ID 403222702 / SFB 1381
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INBS-05-01
German Research Foundation (DFG)	Germany	SCHI 871/11-1

Revision History (Full details and data files)

Version 1.0: 2022-05-18
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

7QHM | pdb_00007qhm

Cytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV2) from Corynebacterium glutamicum (stigmatellin and azide bound)

Literature

Structural basis for safe and efficient energy conversion in a respiratory supercomplex.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)