7QHO | pdb_00007qho

Cytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV2) from Corynebacterium glutamicum (as isolated)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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) Nature Communications 13: 545

  • DOI: https://doi.org/10.1038/s41467-022-28179-x
  • Primary Citation of 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.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex Rieske iron-sulfur subunit
A, N
408Corynebacterium glutamicum ATCC 13032Mutation(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))
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UniProt GroupQ79VE8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome b subunit
B, O
539Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome c subunit
C, P
283Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
D, Q
594Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2
E, R
331Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
F, S
205Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 4
G, T
143Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Cgl2664/cg2949
H, U
163Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized membrane protein Cgl2017/cg2211
I, V
147Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical membrane protein
J, W
112Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Actinobacterial supercomplex, subunit C (AscC)
K, X
73Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical membrane protein
L, Y
65Corynebacterium glutamicum ATCC 13032Mutation(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))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Thiamine biosynthesis protein X
M, Z
168Corynebacterium glutamicum ATCC 13032Mutation(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 
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Small Molecules
Ligands 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IZL (Subject of Investigation/LOI)
Query on IZL
Download Ideal Coordinates CCD File 
BA [auth A],
QB [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
CDL (Subject of Investigation/LOI)
Query on CDL
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EB [auth F]
FB [auth G]
GC [auth Q]
HC [auth Q]
IB [auth I]
EB [auth F],
FB [auth G],
GC [auth Q],
HC [auth Q],
IB [auth I],
JA [auth B],
NA [auth C],
QC [auth S],
RC [auth S],
VA [auth D],
WA [auth D],
WC [auth V],
XB [auth O],
ZB [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
IX7 (Subject of Investigation/LOI)
Query on IX7
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JB [auth I],
OC [auth R]		[(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
HAS (Subject of Investigation/LOI)
Query on HAS
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CC [auth Q],
DC [auth Q],
RA [auth D],
SA [auth D]		HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-ZOMLSHGTSA-L
9YF (Subject of Investigation/LOI)
Query on 9YF
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CA [auth A],
LA [auth B],
RB [auth N],
VC [auth U]		(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
MQ9 (Subject of Investigation/LOI)
Query on MQ9
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DA [auth A]
FA [auth B]
IA [auth B]
NB [auth N]
TB [auth O]
DA [auth A],
FA [auth B],
IA [auth B],
NB [auth N],
TB [auth O],
WB [auth O]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
3PE (Subject of Investigation/LOI)
Query on 3PE
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CB [auth E]
DB [auth F]
EA [auth A]
IC [auth Q]
KB [auth J]
CB [auth E],
DB [auth F],
EA [auth A],
IC [auth Q],
KB [auth J],
NC [auth R],
OB [auth N],
PC [auth S],
XA [auth D],
XC [auth W]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
3PH (Subject of Investigation/LOI)
Query on 3PH
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QA [auth C],
SC [auth T]		1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA (Subject of Investigation/LOI)
Query on DGA
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BB [auth E]
GB [auth H]
LB [auth M]
MC [auth R]
TC [auth U]
BB [auth E],
GB [auth H],
LB [auth M],
MC [auth R],
TC [auth U],
YC [auth Z]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEC (Subject of Investigation/LOI)
Query on HEC
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AC [auth P],
BC [auth P],
OA [auth C],
PA [auth C]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM
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GA [auth B],
HA [auth B],
UB [auth O],
VB [auth O]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LYC (Subject of Investigation/LOI)
Query on LYC
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KA [auth B],
YB [auth O]		LYCOPENE
C40 H56
OAIJSZIZWZSQBC-GYZMGTAESA-N
LMT
Query on LMT
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MA [auth B],
SB [auth O]		DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PLM (Subject of Investigation/LOI)
Query on PLM
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HB [auth H],
MB [auth M],
UC [auth U],
ZC [auth Z]		PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES
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AA [auth A],
PB [auth N]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CUA (Subject of Investigation/LOI)
Query on CUA
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AB [auth E],
KC [auth R],
LC [auth R],
ZA [auth E]		DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU
Download Ideal Coordinates CCD File 
EC [auth Q],
TA [auth D]		COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN
Download Ideal Coordinates CCD File 
JC [auth R],
YA [auth E]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA
Download Ideal Coordinates CCD File 
FC [auth Q],
UA [auth D]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONcisTEM1.0.0

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyBIOSS EXC-294
German Research Foundation (DFG)GermanyCIBSS EXC-2189 Project ID 390939984
German Research Foundation (DFG)GermanyProject-ID 403222702 / SFB 1381
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05-01
German Research Foundation (DFG)GermanySCHI 871/11-1

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary