6J5J

Cryo-EM structure of the mammalian E-state ATP synthase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1.

Gu, J.Zhang, L.Zong, S.Guo, R.Liu, T.Yi, J.Wang, P.Zhuo, W.Yang, M.

(2019) Science 364: 1068-1075

  • DOI: https://doi.org/10.1126/science.aaw4852
  • Primary Citation of Related Structures:  
    6J54, 6J5A, 6J5I, 6J5J, 6J5K

  • PubMed Abstract: 

    The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom resolution using a single-particle cryo-electron microscopy method. Two classical V-shaped ATP synthase dimers lie antiparallel to each other to form an H-shaped ATP synthase tetramer, as viewed from the matrix. ATP synthase inhibitory factor subunit 1 (IF1) is a well-known in vivo inhibitor of mammalian ATP synthase at low pH. Two IF1 dimers link two ATP synthase dimers, which is consistent with the ATP synthase tetramer adopting an inhibited state. Within the tetramer, we refined structures of intact ATP synthase in two different rotational conformations at 3.34- and 3.45-Å resolution.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha, mitochondrial
A, B, C
509Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F
469Sus scrofaMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for K7GLT8 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase inhibitor, mitochondrialG [auth J]83Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gammaH [auth G]272Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrialI [auth H]132Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F1 subunit epsilonJ [auth I]48Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit O, mitochondrialK [auth S]187Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase peripheral stalk-membrane subunit bL [auth b]209Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase-coupling factor 6, mitochondrialM [auth c]70Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialN [auth d]147Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit eO [auth e]63Sus scrofaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit f, mitochondrialP [auth f]87Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gQ [auth g]84Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase membrane subunit DAPITR [auth i]42Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
subunit k analogS [auth k]29Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase protein 8T [auth 8]67Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aU [auth a]226Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial H+ transporting ATP synthase subunit c isoform 172Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase membrane subunit 6.8PLDA [auth u]42Sus scrofaMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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EA [auth A],
GA [auth B],
IA [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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KA [auth D],
MA [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFA0504600 and 2016YFA0501100
National Natural Science Foundation of ChinaChina31625008
National Natural Science Foundation of ChinaChina21532004, 31570733 and 31800620

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations