7QHM

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


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 1.0 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

  • DOI: 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 ...

    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

    CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. carola.hunte@biochemie.uni-freiburg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bc1 complex Rieske iron-sulfur subunitA, N408Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: qcrACgl2190cg2404
Membrane Entity: Yes 
UniProt
Find proteins for Q79VE8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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UniProt GroupQ79VE8
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome b subunitB, O539Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: qcrBCgl2189cg2403
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for Q79VE9 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome c subunitC, P283Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: qcrCCgl2191cg2405
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for Q8NNK5 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1D, Q594Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: ctaDCgl2523cg2780
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for Q79VD7 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2E, R331Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: ctaCCgl2195cg2409
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for Q8NNK2 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3F, S205Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: ctaECgl2192cg2406
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for Q9AEL8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 4G, T143Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: ctaFCgl2194cg2408
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for Q8NNK3 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein Cgl2664/cg2949H, U163Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl2664cg2949
Membrane Entity: Yes 
UniProt
Find proteins for Q8NMB4 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized membrane protein Cgl2017/cg2211I, V147Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl2017cg2211
Membrane Entity: Yes 
UniProt
Find proteins for Q8NP09 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical membrane proteinJ, W112Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl0373
Membrane Entity: Yes 
UniProt
Find proteins for Q8NTD4 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Actinobacterial supercomplex, subunit C (AscC)K, X73Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl0818
UniProt
Find proteins for Q8NS61 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical membrane proteinL, Y65Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl0673
Membrane Entity: Yes 
UniProt
Find proteins for Q8NSJ8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Thiamine biosynthesis protein XM, Z168Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: thiXCgl2332cg2561
Membrane Entity: Yes 
UniProt
Find proteins for P42461 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
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Small Molecules
Ligands 21 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IZL (Subject of Investigation/LOI)
Query on IZL

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
CDL (Subject of Investigation/LOI)
Query on CDL

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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
 Ligand Interaction
IX7 (Subject of Investigation/LOI)
Query on IX7

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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
 Ligand Interaction
HAS (Subject of Investigation/LOI)
Query on HAS

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GC [auth Q],
HC [auth Q],
SA [auth D],
TA [auth D]
HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-QIHJKJTBDH
 Ligand Interaction
9YF (Subject of Investigation/LOI)
Query on 9YF

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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
 Ligand Interaction
MQ9 (Subject of Investigation/LOI)
Query on MQ9

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AC [auth O],
DA [auth A],
IA [auth B],
RB [auth N]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
 Ligand Interaction
3PE (Subject of Investigation/LOI)
Query on 3PE

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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
 Ligand Interaction
DGA (Subject of Investigation/LOI)
Query on DGA

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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
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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DC [auth P],
EC [auth P],
OA [auth C],
PA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
GA [auth B],
HA [auth B],
YB [auth O],
ZB [auth O]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
LYC (Subject of Investigation/LOI)
Query on LYC

Download Ideal Coordinates CCD File 
CC [auth O],
LA [auth B]
LYCOPENE
C40 H56
OAIJSZIZWZSQBC-GYZMGTAESA-N
 Ligand Interaction
SMA (Subject of Investigation/LOI)
Query on SMA

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FA [auth B],
XB [auth O]
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
LMT
Query on LMT

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MA [auth B],
WB [auth O]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
PLM (Subject of Investigation/LOI)
Query on PLM

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DD [auth U],
JB [auth H],
JD [auth Z],
QB [auth M]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
AA [auth A],
TB [auth N]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
CUA (Subject of Investigation/LOI)
Query on CUA

Download Ideal Coordinates CCD File 
BB [auth E],
CB [auth E],
QC [auth R],
RC [auth R]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
IC [auth Q],
UA [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
PC [auth R],
VA [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
AZI (Subject of Investigation/LOI)
Query on AZI

Download Ideal Coordinates CCD File 
KC [auth Q],
XA [auth D]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
JC [auth Q],
WA [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
OXY (Subject of Investigation/LOI)
Query on OXY

Download Ideal Coordinates CCD File 
LC [auth Q]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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