6LOD

Cryo-EM structure of the air-oxidized photosynthetic alternative complex III from Roseiflexus castenholzii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Cryo-EM structures of the air-oxidized and dithionite-reduced photosynthetic alternative complex III from Roseiflexus castenholzii .

Shi, Y.Xin, Y.Wang, C.Blankenship, R.E.Sun, F.Xu, X.

(2020) Sci Adv 6: eaba2739-eaba2739

  • DOI: https://doi.org/10.1126/sciadv.aba2739
  • Primary Citation of Related Structures:  
    6LOD, 6LOE

  • PubMed Abstract: 

    Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation in both the respiratory and photosynthetic electron transport chains of bacteria. The coupling mechanism, however, is poorly understood. Here, we report the cryo-EM structures of air-oxidized and dithionite-reduced ACIII from the photosynthetic bacterium Roseiflexus castenholzii at 3.3- and 3.5-Å resolution, respectively. We identified a menaquinol binding pocket and an electron transfer wire comprising six hemes and four iron-sulfur clusters that is capable of transferring electrons to periplasmic acceptors. We detected a proton translocation passage in which three strictly conserved, mid-passage residues are likely essential for coupling the redox-driven proton translocation across the membrane. These results allow us to propose a previously unrecognized coupling mechanism that links the respiratory and photosynthetic functions of ACIII. This study provides a structural basis for further investigation of the energy transformation mechanisms in bacterial photosynthesis and respiration.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, National Center of Protein Science-Beijing, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MULTIHEME_CYTC domain-containing protein226Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A7NJ87 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
Explore A7NJ87 
Go to UniProtKB:  A7NJ87
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NJ87
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fe-S-cluster-containing hydrogenase components 1-like protein933Roseiflexus castenholzii DSM 13941Mutation(s): 0 
UniProt
Find proteins for A7NJ88 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
Explore A7NJ88 
Go to UniProtKB:  A7NJ88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NJ88
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polysulphide reductase NrfD471Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A7NJ89 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
Explore A7NJ89 
Go to UniProtKB:  A7NJ89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NJ89
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein ActD192Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A7NJ90 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
Explore A7NJ90 
Go to UniProtKB:  A7NJ90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NJ90
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c domain-containing protein162Roseiflexus castenholzii DSM 13941Mutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for A7NJ91 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
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Go to UniProtKB:  A7NJ91
Entity Groups  
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UniProt GroupA7NJ91
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein ActF414Roseiflexus castenholzii DSM 13941Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A7NJ92 (Roseiflexus castenholzii (strain DSM 13941 / HLO8))
Explore A7NJ92 
Go to UniProtKB:  A7NJ92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7NJ92
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC (Subject of Investigation/LOI)
Query on HEC

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
R [auth E]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
EL6
Query on EL6

Download Ideal Coordinates CCD File 
L [auth B],
Q [auth E]
[(2S)-2-octadecanoyloxypropyl] octadecanoate
C39 H76 O4
JEMDXOYRWHZUCG-QNGWXLTQSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
M [auth B],
N [auth B],
O [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S (Subject of Investigation/LOI)
Query on F3S

Download Ideal Coordinates CCD File 
P [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31570738
National Natural Science Foundation of China (NSFC)China31870740
National Natural Science Foundation of China (NSFC)China31400630
Chinese Academy of SciencesChinaXDB08030202
Ministry of Science and Technology (MoST, China)China2017YFA0504700

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release