9ITR | pdb_00009itr

Chloroflexus aurantiacus ATP synthase, state 3, focused refinement of FO and peripheral stalk


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of ATP synthase from an early photosynthetic bacterium Chloroflexus aurantiacus.

Zhang, X.Wu, J.Min, Z.Wang, J.Hong, X.Pei, X.Rao, Z.Xu, X.

(2025) Proc Natl Acad Sci U S A 122: e2425824122-e2425824122

  • DOI: https://doi.org/10.1073/pnas.2425824122
  • Primary Citation of Related Structures:  
    9ITJ, 9ITK, 9ITL, 9ITM, 9ITN, 9ITO, 9ITP, 9ITQ, 9ITR, 9ITS, 9ITT, 9ITU, 9ITV, 9ITW, 9ITX, 9ITY, 9ITZ, 9IU0

  • PubMed Abstract: 

    F-type ATP synthase (F 1 F O ) catalyzes proton motive force-driven ATP synthesis in mitochondria, chloroplasts, and bacteria. Different from the mitochondrial and bacterial enzymes, F 1 F O from photosynthetic organisms have evolved diverse structural and mechanistic details to adapt to the light-dependent reactions. Although complete structure of chloroplast F 1 F O has been reported, no high-resolution structure of an F 1 F O from photosynthetic bacteria has been available. Here, we report cryo-EM structures of an intact and functionally competent F 1 F O from Chloroflexus aurantiacus ( Ca F 1 F O ), a filamentous anoxygenic phototrophic bacterium from the earliest branch of photosynthetic organisms. The structures of Ca F 1 F O in its ADP-free and ADP-bound forms for three rotational states reveal a previously unrecognized architecture of ATP synthases. A pair of peripheral stalks connect to the Ca F 1 head through a dimer of δ-subunits, and associate with two membrane-embedded a-subunits that are asymmetrically positioned outside and clamp Ca F O 's c 10 -ring. The two a-subunits constitute two proton inlets on the periplasmic side and two proton outlets on the cytoplasmic side, endowing Ca F 1 F O with unique proton translocation pathways that allow more protons being translocated relative to single a-subunit F 1 F O . Our findings deepen understanding of the architecture and proton translocation mechanisms of F 1 F O synthases and suggest innovative strategies for modulating their activities by altering the number of a-subunit.


  • 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c76Chloroflexus aurantiacus J-10-flMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9WGS9 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Explore A9WGS9 
Go to UniProtKB:  A9WGS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WGS9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aK [auth T],
L [auth Z]
312Chloroflexus aurantiacus J-10-flMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9WGT0 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Explore A9WGT0 
Go to UniProtKB:  A9WGT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WGT0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bM [auth Y],
N [auth V],
O [auth U],
P [auth X]
164Chloroflexus aurantiacus J-10-flMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9WGS8 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Explore A9WGS8 
Go to UniProtKB:  A9WGS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WGS8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171227, 31870740,31570738

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references