5LQX

Structure of F-ATPase from Pichia angusta, state3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 of the entry. See complete history


Literature

Structure of the mitochondrial ATP synthase fromPichia angustadetermined by electron cryo-microscopy.

Vinothkumar, K.R.Montgomery, M.G.Liu, S.Walker, J.E.

(2016) Proc Natl Acad Sci U S A 113: 12709-12714

  • DOI: https://doi.org/10.1073/pnas.1615902113
  • Primary Citation of Related Structures:  
    5LQX, 5LQY, 5LQZ

  • PubMed Abstract: 

    The structure of the intact monomeric ATP synthase from the fungus, Pichia angusta , has been solved by electron cryo-microscopy. The structure provides insights into the mechanical coupling of the transmembrane proton motive force across mitochondrial membranes in the synthesis of ATP. This mechanism requires a strong and integral stator, consisting of the catalytic α 3 β 3 -domain, peripheral stalk, and, in the membrane domain, subunit a and associated supernumerary subunits, kept in contact with the rotor turning at speeds up to 350 Hz. The stator's integrity is ensured by robust attachment of both the oligomycin sensitivity conferral protein (OSCP) to the catalytic domain and the membrane domain of subunit b to subunit a. The ATP8 subunit provides an additional brace between the peripheral stalk and subunit a. At the junction between the OSCP and the apparently stiff, elongated α-helical b-subunit and associated d- and h-subunits, an elbow or joint allows the stator to bend to accommodate lateral movements during the activity of the catalytic domain. The stator may also apply lateral force to help keep the static a-subunit and rotating c 10 -ring together. The interface between the c 10 -ring and the a-subunit contains the transmembrane pathway for protons, and their passage across the membrane generates the turning of the rotor. The pathway has two half-channels containing conserved polar residues provided by a bundle of four α-helices inclined at ∼30° to the plane of the membrane, similar to those described in other species. The structure provides more insights into the workings of this amazing machine.


  • Organizational Affiliation

    The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit fA [auth 1]31Ogataea angustaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase AAP1 subunitB [auth 2]25Ogataea angustaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aC [auth 3]17Ogataea angustaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bD [auth 4]27Ogataea angustaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase alpha subunitE [auth A],
F [auth B],
G [auth C]
510Ogataea angustaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W1Q6W1 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
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Find proteins for C0HK51 (Pichia angusta)
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UniProt GroupsW1Q6W1C0HK51
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase beta subunitH [auth D],
I [auth E],
J [auth F]
476Ogataea angustaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W1QA59 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
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UniProt GroupW1QA59
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma subunitK [auth G]269Ogataea angustaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for C0HK53 (Pichia angusta)
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Find proteins for W1QGS3 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
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UniProt GroupsW1QGS3C0HK53
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase delta subunitL [auth H]138Ogataea angustaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon subunitM [auth I]63Ogataea angustaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1L1QK34 (Pichia angusta)
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UniProt GroupA0A1L1QK34
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase inhibitor protein IF1N [auth J]66Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c76Ogataea angustaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupC0HK59
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase OSCP subunitY [auth U]194Ogataea angustaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W1QCI5 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
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Find proteins for C0HK56 (Pichia angusta)
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UniProt GroupsC0HK56W1QCI5
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bZ [auth V]204Ogataea angustaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for C0HK58 (Pichia angusta)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit dAA [auth W]155Ogataea angustaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for C0HK60 (Pichia angusta)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit hBA [auth X]21Ogataea angustaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aCA [auth Y]252Ogataea angustaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for C0HK57 (Pichia angusta)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aDA [auth Z]44Ogataea angustaMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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EA [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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GA [auth B],
IA [auth C],
KA [auth D],
MA [auth E],
NA [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

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FA [auth A],
HA [auth B],
JA [auth C],
LA [auth D],
OA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.3: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references