6TT7

Ovine ATP synthase 1a state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Cryo-EM structure of the entire mammalian F-type ATP synthase.

Pinke, G.Zhou, L.Sazanov, L.A.

(2020) Nat Struct Mol Biol 27: 1077-1085

  • DOI: 10.1038/s41594-020-0503-8
  • Primary Citation of Related Structures:  
    6ZA9, 6TT7

  • PubMed Abstract: 
  • The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy ...

    The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the 'proton translocation cluster' attached to the c-ring and a more distant 'hook apparatus' holding subunit e. Unexpectedly, this subunit is anchored to a lipid 'plug' capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.


    Organizational Affiliation

    Institute of Science and Technology Austria, Klosterneuburg, Austria. sazanov@ist.ac.at.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit alphaC [auth A], A [auth B], B [auth C]553Ovis ariesMutation(s): 0 
Gene Names: ATP5F1A
Membrane Entity: Yes 
UniProt
Find proteins for W5NY50 (Ovis aries)
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit betaE [auth D], D [auth E], F528Ovis ariesMutation(s): 0 
Gene Names: ATP5F1B
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for W5PEP7 (Ovis aries)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit gammaG298Ovis ariesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase F1 subunit deltaH168Ovis ariesMutation(s): 0 
Gene Names: ATP5F1D
Membrane Entity: Yes 
UniProt
Find proteins for W5PP03 (Ovis aries)
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase F1 subunit epsilonI51Ovis ariesMutation(s): 0 
Gene Names: ATP5F1E
UniProt
Find proteins for W5Q3H8 (Ovis aries)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase peripheral stalk subunit OSCPJ213Ovis ariesMutation(s): 0 
Gene Names: ATP5O
Membrane Entity: Yes 
UniProt
Find proteins for B9VH06 (Ovis aries)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit bK256Ovis ariesMutation(s): 0 
Gene Names: ATP5PB
Membrane Entity: Yes 
UniProt
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  • Reference Sequence
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase-coupling factor 6, mitochondrialL108Ovis ariesMutation(s): 0 
Gene Names: ATP5PF
Membrane Entity: Yes 
UniProt
Find proteins for W5Q0Q5 (Ovis aries)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialM161Ovis ariesMutation(s): 0 
Gene Names: ATP5PD
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit C1, mitochondrialN [auth 1], O [auth 2], P [auth 3], Q [auth 4], R [auth 5], S [auth 6], T [auth 7], U [auth 8]136Ovis ariesMutation(s): 0 
Gene Names: ATP5MC1ATP5G1
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit aV [auth N]226Ovis ariesMutation(s): 0 
Gene Names: MT-ATP6ATP6ATPASE6MTATP6
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit DAPITW [auth O]58Ovis ariesMutation(s): 0 
Gene Names: LOC114117623
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase membrane subunit 6.8PLX [auth P]60Ovis ariesMutation(s): 0 
Gene Names: ATP5MPL
UniProt
Find proteins for W5P913 (Ovis aries)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase protein 8Y [auth Q]66Ovis ariesMutation(s): 0 
Gene Names: MT-ATP8ATP8ATPASE8MTATP8
Membrane Entity: Yes 
UniProt
Find proteins for O78751 (Ovis aries)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase membrane subunit fZ [auth R]88Ovis ariesMutation(s): 0 
Gene Names: PTCD1
Membrane Entity: Yes 
UniProt
Find proteins for W5QB48 (Ovis aries)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunitAA [auth S]103Ovis ariesMutation(s): 0 
Gene Names: LOC101118348
Membrane Entity: Yes 
UniProt
Find proteins for W5Q5U7 (Ovis aries)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit eBA [auth T]71Ovis ariesMutation(s): 0 
Gene Names: LOC101102454
Membrane Entity: Yes 
UniProt
Find proteins for W5PF18 (Ovis aries)
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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OA [auth R], PA [auth R], QA [auth R]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
P5S (Subject of Investigation/LOI)
Query on P5S

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MA [auth 2]O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
 Ligand Interaction
LHG (Subject of Investigation/LOI)
Query on LHG

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KA [auth K], LA [auth K], NA [auth 2], RA [auth R], SA [auth S], TA [auth S]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
S12 (Subject of Investigation/LOI)
Query on S12

Download Ideal Coordinates CCD File 
UA [auth T]O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine
C24 H46 N O9 P
JZWNYZVVZXZRRH-VXKWHMMOSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

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DA [auth B], FA [auth C], HA [auth A], IA [auth D], JA [auth F]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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CA [auth B], EA [auth C], GA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 2.0: 2020-12-30
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary