9ILT | pdb_00009ilt

Crystal structure of alternative complex III from Chloroflexus aurantiacus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 
    0.286 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.249 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

Starting Model: experimental
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Literature

Crystal structure of the alternative complex III from the phototrophic bacterium Chloroflexus aurantiacus.

Wu, W.Fang, H.He, H.Wu, J.Gong, Z.Li, C.Pei, X.Xu, X.

(2025) Structure 33: 29-38.e2

  • DOI: https://doi.org/10.1016/j.str.2024.10.014
  • Primary Citation of Related Structures:  
    9ILT

  • PubMed Abstract: 

    Alternative complex III (ACIII) is a multi-subunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation in bacterial respiratory and photosynthetic electron transport chains. Four ACIII cryoelectron microscopy (cryo-EM) structures are known. However, the effects of cryo-EM versus X-ray crystallography structure determination on ACIII structure are unclear. Here, we report a 3.25 Å crystal structure of photosynthetic ACIII from Chloroflexus aurantiacus (CaACIIIp), revealing eight subunits (ActA-G and I) with four iron-sulfur clusters and six c-type hemes, a menaquinol-binding site, and two proton translocation passages. Structural comparisons with the previously reported cryo-EM structures reveal slight local conformational changes in the solvent-exposed regions of ActB, ActD, ActG, and the transmembrane (TM) helix of subunit I. The regions conferring structural flexibility possess low sequence conservation across species. However, the core functional modules containing the menaquinol-binding pocket, redox centers, and proton translocation passages remain unchanged, preserving the enzyme's activity.


  • Organizational Affiliation
    • Zhejiang Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c7-like domain-containing protein219Chloroflexus aurantiacus J-10-flMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9WEV2 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Explore A9WEV2 
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WEV2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fe-S-cluster-containing hydrogenase components 1-like protein1,029Chloroflexus aurantiacus J-10-flMutation(s): 0 
UniProt
Find proteins for A9WEV3 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WEV3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polysulphide reductase NrfD486Chloroflexus aurantiacus J-10-flMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9WEV4 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
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UniProt GroupA9WEV4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Quinol:cytochrome c oxidoreductase membrane protein179Chloroflexus aurantiacus J-10-flMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9WEV5 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WEV5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c domain-containing protein205Chloroflexus aurantiacus J-10-flMutation(s): 0 
UniProt
Find proteins for A9WEV6 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
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UniProt GroupA9WEV6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Quinol:cytochrome c oxidoreductase quinone-binding subunit 2411Chloroflexus aurantiacus J-10-flMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9WEV7 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ActG112Chloroflexus aurantiacus J-10-flMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9WEV8 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
subunit IH [auth I]37Chloroflexus aurantiacus J-10-flMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AAN0NP81 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
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UniProt GroupA0AAN0NP81
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth E]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
N [auth B],
O [auth B],
P [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free:  0.286 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.249 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.016α = 90
b = 153.063β = 90
c = 173.381γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-03-19 
  • Deposition Author(s): Xu, X., Wu, W.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870740, 32171227, 31570738, 32000034, 82101628

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release