6J5K

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1126/science.aaw4852
  • Primary Citation of Related Structures:  
    6J54, 6J5J, 6J5I, 6J5K, 6J5A

  • 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 ...

    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

    School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase F1 subunit alpha509Sus scrofaMutation(s): 0 
Gene Names: ATP5F1AATP5A1ATP5A2
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit beta469Sus scrofaMutation(s): 0 
Gene Names: ATP5F1B
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase inhibitor, mitochondrialKA [auth AJ], OB [auth BJ], SC [auth CJ], G [auth J]83Sus scrofaMutation(s): 0 
Gene Names: ATP5IF1ATPIATPIF1
Membrane Entity: Yes 
UniProt
Find proteins for Q29307 (Sus scrofa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit gammaLA [auth AG], PB [auth BG], TC [auth CG], H [auth G]272Sus scrofaMutation(s): 0 
Gene Names: ATP5F1C
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrialMA [auth AH], QB [auth BH], UC [auth CH], I [auth H]132Sus scrofaMutation(s): 0 
Gene Names: ATP5F1D
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase F1 subunit epsilonNA [auth AI], RB [auth BI], VC [auth CI], J [auth I]48Sus scrofaMutation(s): 0 
Gene Names: ATP5ECH242-247L10.5-002
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit O, mitochondrialOA [auth AS], SB [auth BS], WC [auth CS], K [auth S]187Sus scrofaMutation(s): 0 
Gene Names: ATP5POATP5O
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase peripheral stalk-membrane subunit bPA [auth Ab], TB [auth Bb], XC [auth Cb], L [auth b]209Sus scrofaMutation(s): 0 
Gene Names: ATP5PB
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase-coupling factor 6, mitochondrialQA [auth Ac], UB [auth Bc], YC [auth Cc], M [auth c]70Sus scrofaMutation(s): 0 
Gene Names: ATP5PFATP5J
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialRA [auth Ad], VB [auth Bd], ZC [auth Cd], N [auth d]147Sus scrofaMutation(s): 0 
Gene Names: ATP5PD
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit eSA [auth Ae], WB [auth Be], AD [auth Ce], O [auth e]63Sus scrofaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit f, mitochondrialTA [auth Af], XB [auth Bf], BD [auth Cf], P [auth f]87Sus scrofaMutation(s): 0 
Gene Names: ATP5MFATP5J2
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit gUA [auth Ag], YB [auth Bg], CD [auth Cg], Q [auth g]84Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase membrane subunit DAPITVA [auth Ai], ZB [auth Bi], DD [auth Ci], R [auth i]42Sus scrofaMutation(s): 0 
Gene Names: ATP5MD
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
subunit k analogWA [auth Ak], AC [auth Bk], ED [auth Ck], S [auth k]29Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase protein 8T [auth 8], XA [auth A8], BC [auth B8], FD [auth C8]67Sus scrofaMutation(s): 0 
Gene Names: MT-ATP8ATP8ATPASE8MTATP8
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit aYA [auth Aa], CC [auth Ba], GD [auth Ca], U [auth a]226Sus scrofaMutation(s): 0 
Gene Names: MT-ATP6ATP6ATPASE6MTATP6
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial H+ transporting ATP synthase subunit c isoform 172Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase membrane subunit 6.8PLHB [auth Au], LC [auth Bu], PD [auth Cu], DA [auth u]42Sus scrofaMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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AE [auth AA] , CE [auth AB] , EE [auth AC] , KE [auth BA] , ME [auth BB] , OE [auth BC] , QD [auth A] , SD [auth B] , 
AE [auth AA],  CE [auth AB],  EE [auth AC],  KE [auth BA],  ME [auth BB],  OE [auth BC],  QD [auth A],  SD [auth B],  UD [auth C],  UE [auth CA],  WE [auth CB],  YE [auth CC]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
AF [auth CD], CF, GE [auth AD], IE [auth AF], QE [auth BD], SE [auth BF], WD [auth D], YD [auth F]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BE [auth AA] , BF [auth CD] , DE [auth AB] , DF [auth CF] , FE [auth AC] , HE [auth AD] , JE [auth AF] , LE [auth BA] , 
BE [auth AA],  BF [auth CD],  DE [auth AB],  DF [auth CF],  FE [auth AC],  HE [auth AD],  JE [auth AF],  LE [auth BA],  NE [auth BB],  PE [auth BC],  RD [auth A],  RE [auth BD],  TD [auth B],  TE [auth BF],  VD [auth C],  VE [auth CA],  XD [auth D],  XE [auth CB],  ZD [auth F],  ZE [auth CC]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 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