8K9F

Cryo-EM structure of the photosynthetic alternative complex III from Chloroflexus aurantiacus at 2.9 angstrom


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structure of HQNO-bound Alternative Complex III from the anoxygenic phototrophic bacterium Chloroflexus aurantiacus.

Xin, J.Min, Z.Yu, L.Yuan, X.Liu, A.Wu, W.Zhang, X.He, H.Wu, J.Xin, Y.Blankenship, R.E.Tian, C.Xu, X.

(2024) Plant Cell 

  • DOI: https://doi.org/10.1093/plcell/koae029
  • Primary Citation of Related Structures:  
    8K9E, 8K9F, 8X2J

  • PubMed Abstract: 

    Alternative complex III (ACIII) couples quinol oxidation and electron acceptor reduction with potential transmembrane proton translocation. It is compositionally and structurally different from the cytochrome bc1/b6f complexes, but functionally replaces these enzymes in the photosynthetic and/or respiratory electron transport chains (ETCs) of many bacteria. However, the true compositions and architectures of ACIIIs remain unclear, as do their structural and functional relevance in mediating the ETCs. We here determined cryogenic electron microscopy structures of photosynthetic ACIII isolated from Chloroflexus aurantiacus (CaACIIIp), in apo-form and in complexed form bound to a menadiol analog 2-heptyl-4-hydroxyquinoline-N-oxide (HQNO). Besides six canonical subunits (ActABCDEF), the structures revealed conformations of two previously unresolved subunits, ActG and I, which contributed to the complex stability. We also elucidated the structural basis of menaquinol oxidation and subsequent electron transfer along the [3Fe-4S]-6 hemes wire to its periplasmic electron acceptors, using electron paramagnetic resonance (EPR), spectroelectrochemistry, enzymatic analyses and molecular dynamics (MD) simulations. A unique insertion loop in ActE was shown to function in determining the binding specificity of CaACIIIp for downstream electron acceptors. This study broadens our understanding of the structural diversity and molecular evolution of ACIIIs, enabling further investigation of the (mena)quinol oxidoreductases evolved coupling mechanism in bacterial energy conservation.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and The Affiliated Hospital, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, 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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UniProt GroupA9WEV2
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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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Go to UniProtKB:  A9WEV5
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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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Go to UniProtKB:  A9WEV6
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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))
Explore A9WEV7 
Go to UniProtKB:  A9WEV7
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UniProt GroupA9WEV7
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
hypothetical protein112Chloroflexus 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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UniProt GroupA9WEV8
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
unknownH [auth I]37Chloroflexus aurantiacus J-10-flMutation(s): 0 
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JM9
Query on JM9

Download Ideal Coordinates CCD File 
V [auth F]1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate
C48 H92 O6
FXZBBNDITVPQLC-UHFFFAOYSA-N
JL3
Query on JL3

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U [auth F][(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate
C35 H70 N O8 P
SKVKIGSFTGVBOX-MGBGTMOVSA-N
JLQ
Query on JLQ

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S [auth C][(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate
C35 H70 N O8 P
MMLCPRRXWWDUCM-MGBGTMOVSA-N
HEC
Query on HEC

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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],
T [auth E]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SF4
Query on SF4

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

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Q [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
MG
Query on MG

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R [auth B]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

  • Released Date: 2024-03-06 
  • Deposition Author(s): Xu, X.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release