7Q21

III2-IV2 respiratory supercomplex from Corynebacterium glutamicum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The respiratory supercomplex from C. glutamicum.

Moe, A.Kovalova, T.Krol, S.Yanofsky, D.J.Bott, M.Sjostrand, D.Rubinstein, J.L.Hogbom, M.Brzezinski, P.

(2022) Structure 30: 338

  • DOI: https://doi.org/10.1016/j.str.2021.11.008
  • Primary Citation of Related Structures:  
    7Q21

  • PubMed Abstract: 

    Corynebacterium glutamicum is a preferentially aerobic gram-positive bacterium belonging to the phylum Actinobacteria, which also includes the pathogen Mycobacterium tuberculosis. In these bacteria, respiratory complexes III and IV form a CIII 2 CIV 2 supercomplex that catalyzes oxidation of menaquinol and reduction of dioxygen to water. We isolated the C. glutamicum supercomplex and used cryo-EM to determine its structure at 2.9 Å resolution. The structure shows a central CIII 2 dimer flanked by a CIV on two sides. A menaquinone is bound in each of the Q N and Q P sites in each CIII and an additional menaquinone is positioned ∼14 Å from heme b L . A di-heme cyt. cc subunit electronically connects each CIII with an adjacent CIV, with the Rieske iron-sulfur protein positioned with the iron near heme b L . Multiple subunits interact to form a convoluted sub-structure at the cytoplasmic side of the supercomplex, which defines a path for proton transfer into CIV.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Co-purified unknown transmembrane helices built as polyALA (AscD)A [auth Y],
K [auth y]
96Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3B [auth E],
L [auth e]
205Corynebacterium 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 / 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
Uncharacterized membrane protein Cgl2017/cg2211C [auth H],
M [auth h]
147Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl2017cg2211
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 4D [auth F],
N [auth f]
143Corynebacterium 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 / 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 2E [auth G],
O [auth g]
359Corynebacterium 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 / 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 1F [auth D],
P [auth d]
594Corynebacterium 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 / 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 bc1 complex Rieske iron-sulfur subunitG [auth A],
Q [auth a]
408Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: qcrACgl2190cg2404
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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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Cgl2664/cg2949H [auth L],
R [auth l]
194Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl2664cg2949
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
Cytochrome bc1 complex cytochrome b subunitI [auth B],
S [auth b]
539Corynebacterium 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 / 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
Cytochrome bc1 complex cytochrome c subunitJ [auth C],
T [auth c]
283Corynebacterium 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 / 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
Co-purified unknown peptide built as polyALA (AscE)U [auth X]21Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Co-purified unknown peptide built as polyALA (AscE)V [auth x]22Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Actinobacterial supercomplex, subunit C (AscC)W [auth V],
X [auth v]
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: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical membrane proteinY [auth K],
Z [auth k]
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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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AA [auth E]
BC [auth f]
BD [auth b]
GD [auth b]
HA [auth F]
AA [auth E],
BC [auth f],
BD [auth b],
GD [auth b],
HA [auth F],
ID [auth c],
KC [auth d],
MB [auth B],
OB [auth B],
QB [auth C],
QC [auth d],
RA [auth D],
TB [auth e],
WA [auth D]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HAS
Query on HAS

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MC [auth d],
NC [auth d],
SA [auth D],
TA [auth D]
HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-ZOMLSHGTSA-L
9YF
Query on 9YF

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AD [auth l],
GB [auth L],
VC [auth a],
YC [auth a]
(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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EB [auth A]
ED [auth b]
FD [auth b]
KB [auth B]
LB [auth B]
EB [auth A],
ED [auth b],
FD [auth b],
KB [auth B],
LB [auth B],
WC [auth a]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
HEC
Query on HEC

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JD [auth c],
KD [auth c],
RB [auth C],
SB [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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CD [auth b],
DD [auth b],
IB [auth B],
JB [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
9XX
Query on 9XX

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EA [auth H],
PB [auth B],
XB [auth h],
ZB [auth h]
(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
C38 H74 O4
LWLNRPPCJIGPLI-ZPGRZCPFSA-N
7PH
Query on 7PH

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AB [auth D]
BA [auth E]
DA [auth H]
GC [auth f]
JC [auth g]
AB [auth D],
BA [auth E],
DA [auth H],
GC [auth f],
JC [auth g],
MA [auth F],
ND [auth k],
PA [auth G],
RC [auth d],
SC [auth d],
TC [auth d],
UB [auth e],
WB [auth h],
XA [auth D],
YA [auth D],
ZA [auth D]
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
TWT
Query on TWT

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FA [auth H],
YB [auth h]
DOCOSANE
C22 H46
HOWGUJZVBDQJKV-UHFFFAOYSA-N
PLM
Query on PLM

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HB [auth L],
LD [auth X],
MD [auth x],
UC [auth d]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
TRD
Query on TRD

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AC [auth f]
CA [auth E]
CB [auth A]
CC [auth f]
DB [auth A]
AC [auth f],
CA [auth E],
CB [auth A],
CC [auth f],
DB [auth A],
DC [auth f],
EC [auth f],
FB [auth A],
FC [auth f],
GA [auth F],
HD [auth b],
IA [auth F],
JA [auth F],
KA [auth F],
LA [auth F],
NB [auth B],
VB [auth e],
ZC [auth a]
TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
FES
Query on FES

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BB [auth A],
XC [auth a]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU
Query on CU

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HC [auth g]
IC [auth g]
NA [auth G]
OA [auth G]
OC [auth d]
HC [auth g],
IC [auth g],
NA [auth G],
OA [auth G],
OC [auth d],
UA [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA
Query on CA

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PC [auth d],
VA [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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LC [auth d],
QA [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationCanada--
Swedish Research CouncilCanada--
Canadian Institutes of Health Research (CIHR)CanadaPJT162186
Canada Research ChairsCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary