6HWH | pdb_00006hwh

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

Validation slider image for 6HWH

This is version 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 710.3 kDa 
  • Atom Count: 40,632 
  • Modeled Residue Count: 5,304 
  • Deposited Residue Count: 6,388 
  • Unique protein chains: 13

Macromolecules

Find similar proteins by:|  3D Structure
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))
Explore A0R051 
Go to UniProtKB:  A0R051
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R051
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 
Find similar proteins by:|  3D Structure
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 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Co-purified unknown peptide built as polyALAD [auth I],
Q [auth E]
20Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Co-purified unknown peptide built as polyALAE [auth J],
R [auth F]
35Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Find similar proteins by:|  3D Structure
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 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0R050 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R050 
Go to UniProtKB:  A0R050
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R050
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0R057 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R057 
Go to UniProtKB:  A0R057
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R057
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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))
Explore A0R1B6 
Go to UniProtKB:  A0R1B6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R1B6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein MSMEG_4692/MSMEI_4575I [auth T],
V [auth O]
157Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R1B5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R1B5 
Go to UniProtKB:  A0R1B5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R1B5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0R0M4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R0M4 
Go to UniProtKB:  A0R0M4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R0M4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0R056 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R056 
Go to UniProtKB:  A0R056
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R056
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0R049 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R049 
Go to UniProtKB:  A0R049
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R049
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0R052 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R052 
Go to UniProtKB:  A0R052
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R052
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
DB [auth Y],
EA [auth M],
EB [auth Y],
QA [auth b]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
CA [auth A],
RA [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
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

View Full Validation Report



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
  • Version 1.4: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations, Structure summary