6HWH

Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a functional obligate complex III2IV2respiratory supercomplex from Mycobacterium smegmatis.

Wiseman, B.Nitharwal, R.G.Fedotovskaya, O.Schafer, J.Guo, H.Kuang, Q.Benlekbir, S.Sjostrand, D.Adelroth, P.Rubinstein, J.L.Brzezinski, P.Hogbom, M.

(2018) Nat Struct Mol Biol 25: 1128-1136

  • DOI: https://doi.org/10.1038/s41594-018-0160-3
  • Primary Citation of Related Structures:  
    6HWH

  • PubMed Abstract: 

    In the mycobacterial electron-transport chain, respiratory complex III passes electrons from menaquinol to complex IV, which in turn reduces oxygen, the terminal acceptor. Electron transfer is coupled to transmembrane proton translocation, thus establishing the electrochemical proton gradient that drives ATP synthesis. We isolated, biochemically characterized, and determined the structure of the obligate III 2 IV 2 supercomplex from Mycobacterium smegmatis, a model for Mycobacterium tuberculosis. The supercomplex has quinol:O 2 oxidoreductase activity without exogenous cytochrome c and includes a superoxide dismutase subunit that may detoxify reactive oxygen species produced during respiration. We found menaquinone bound in both the Q o and Q i sites of complex III. The complex III-intrinsic diheme cytochrome cc subunit, which functionally replaces both cytochrome c 1 and soluble cytochrome c in canonical electron-transport chains, displays two conformations: one in which it provides a direct electronic link to complex IV and another in which it serves as an electrical switch interrupting the connection.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden. peterb@dbb.su.se.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunitA,
N [auth B]
408Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R051 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R051
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Co-purified unknown transmembrane helices built as polyALAB [auth G],
O [auth C]
74Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Co-purified unknown transmembrane helices built as polyALAC [auth H],
P [auth D]
65Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Co-purified unknown peptide built as polyALAD [auth I],
Q [auth E]
20Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Co-purified unknown peptide built as polyALAE [auth J],
R [auth F]
35Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome c subunitAA [auth i],
BA [auth j],
F [auth M],
S [auth K]
268Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A0R050 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2G [auth P],
T [auth L]
341Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
MSMEG_4693H [auth R],
U [auth N]
79Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R1B6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R1B6
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein MSMEG_4692/MSMEI_4575I [auth T],
V [auth O]
157Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1J [auth V],
W [auth Q]
583Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for A0R0M4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 4K [auth X],
X [auth S]
139Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3L [auth Z],
Y [auth W]
203Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for A0R049 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase QcrBM [auth b],
Z [auth Y]
554Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: qcrBMSMEI_4163
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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BB [auth Y]
CB [auth Y]
DA [auth M]
LA [auth V]
OA [auth b]
BB [auth Y],
CB [auth Y],
DA [auth M],
LA [auth V],
OA [auth b],
PA [auth b],
SA [auth K],
YA [auth Q]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HAS
Query on HAS

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HA [auth V],
IA [auth V],
VA [auth Q],
WA [auth Q]
HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-ZOMLSHGTSA-L
MQ9
Query on MQ9

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DB [auth Y],
EA [auth M],
EB [auth Y],
QA [auth b]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
HEC
Query on HEC

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FB [auth i],
GB [auth j],
HB [auth j],
KA [auth V]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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AB [auth Y],
MA [auth b],
NA [auth b],
ZA [auth Y]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES
Query on FES

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CA [auth A],
RA [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU
Query on CU

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FA [auth P]
GA [auth P]
JA [auth V]
TA [auth L]
UA [auth L]
FA [auth P],
GA [auth P],
JA [auth V],
TA [auth L],
UA [auth L],
XA [auth Q]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.8.9.1
MODEL REFINEMENTPHENIX1.14-3228-000
RECONSTRUCTIONcryoSPARC2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaMOP 81294
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Data collection, Refinement description