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 1.2 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 F1 subunit alpha509Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta469Sus scrofaMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for K7GLT8 (Sus scrofa)
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UniProt GroupK7GLT8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase inhibitor, mitochondrialG [auth J],
KA [auth AJ],
OB [auth BJ],
SC [auth CJ]
83Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gammaH [auth G],
LA [auth AG],
PB [auth BG],
TC [auth CG]
272Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrialI [auth H],
MA [auth AH],
QB [auth BH],
UC [auth CH]
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],
NA [auth AI],
RB [auth BI],
VC [auth CI]
48Sus scrofaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit O, mitochondrialK [auth S],
OA [auth AS],
SB [auth BS],
WC [auth CS]
187Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase peripheral stalk-membrane subunit bL [auth b],
PA [auth Ab],
TB [auth Bb],
XC [auth Cb]
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],
QA [auth Ac],
UB [auth Bc],
YC [auth Cc]
70Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialN [auth d],
RA [auth Ad],
VB [auth Bd],
ZC [auth Cd]
147Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit eAD [auth Ce],
O [auth e],
SA [auth Ae],
WB [auth Be]
63Sus scrofaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit f, mitochondrialBD [auth Cf],
P [auth f],
TA [auth Af],
XB [auth Bf]
87Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gCD [auth Cg],
Q [auth g],
UA [auth Ag],
YB [auth Bg]
84Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase membrane subunit DAPITDD [auth Ci],
R [auth i],
VA [auth Ai],
ZB [auth Bi]
42Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
subunit k analogAC [auth Bk],
ED [auth Ck],
S [auth k],
WA [auth Ak]
29Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase protein 8BC [auth B8],
FD [auth C8],
T [auth 8],
XA [auth A8]
67Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aCC [auth Ba],
GD [auth Ca],
U [auth a],
YA [auth Aa]
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],
HB [auth Au],
LC [auth Bu],
PD [auth Cu]
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

Download Ideal Coordinates CCD File 
AE [auth AA]
CE [auth AB]
EE [auth AC]
KE [auth BA]
ME [auth BB]
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
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]
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
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]
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
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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