6J5K

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

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Sus scrofa
  • Mutation(s): No 

  • Deposited: 2019-01-11 Released: 2019-06-26 
  • Deposition Author(s): Gu, J., Zhang, L., Yi, J., Yang, M.
  • Funding Organization(s): Ministry of Science and Technology (China), National Natural Science Foundation of China

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 ...

    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 alphaA, AA, AB, AC, B, BA, BB, BC, A,  AA,  AB,  AC,  B,  BA,  BB,  BC,  C,  CA,  CB,  CC
509Sus scrofaMutation(s): 0 
Gene Names: ATP5F1A, ATP5A1, ATP5A2
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for P80021 (Sus scrofa)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit betaAD, AE, AF, BD, BE, BF, CD, CE, AD,  AE,  AF,  BD,  BE,  BF,  CD,  CE,  CF,  D,  E,  F
469Sus scrofaMutation(s): 0 
Gene Names: ATP5F1B
EC: 7.1.2.2
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for K7GLT8 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase inhibitor, mitochondrial AJ, BJ, CJ, J83Sus scrofaMutation(s): 0 
Gene Names: ATP5IF1, ATPI, ATPIF1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for Q29307 (Sus scrofa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit gamma AG, BG, CG, G272Sus scrofaMutation(s): 0 
Gene Names: ATP5F1C
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for A0A287A9I8 (Sus scrofa)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrial AH, BH, CH, H132Sus scrofaMutation(s): 0 
Gene Names: ATP5F1D
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for A0A286ZYL7 (Sus scrofa)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase F1 subunit epsilon AI, BI, CI, I48Sus scrofaMutation(s): 0 
Gene Names: ATP5E, CH242-247L10.5-002
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit O, mitochondrial AS, BS, CS, S187Sus scrofaMutation(s): 0 
Gene Names: ATP5PO, ATP5O
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for Q2EN81 (Sus scrofa)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase peripheral stalk-membrane subunit b Ab, Bb, Cb, b209Sus scrofaMutation(s): 0 
Gene Names: ATP5PB
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for A0A286ZYM6 (Sus scrofa)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase-coupling factor 6, mitochondrial Ac, Bc, Cc, c70Sus scrofaMutation(s): 0 
Gene Names: ATP5PF, ATP5J
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for P13618 (Sus scrofa)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrial Ad, Bd, Cd, d147Sus scrofaMutation(s): 0 
Gene Names: ATP5PD
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for A0A287B4I0 (Sus scrofa)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit e Ae, Be, Ce, e63Sus scrofaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit f, mitochondrial Af, Bf, Cf, f87Sus scrofaMutation(s): 0 
Gene Names: ATP5MF, ATP5J2
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for Q95339 (Sus scrofa)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit g Ag, Bg, Cg, g84Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase membrane subunit DAPIT Ai, Bi, Ci, i42Sus scrofaMutation(s): 0 
Gene Names: ATP5MD
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
subunit k analog Ak, Bk, Ck, k29Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase protein 8 8, A8, B8, C867Sus scrofaMutation(s): 0 
Gene Names: MT-ATP8, ATP8, ATPASE8, MTATP8
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for Q35914 (Sus scrofa)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit a Aa, Ba, Ca, a226Sus scrofaMutation(s): 0 
Gene Names: MT-ATP6, ATP6, ATPASE6, MTATP6
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for Q35915 (Sus scrofa)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial H+ transporting ATP synthase subunit c isoform 1AK, AL, AM, AN, AO, AP, AQ, AR, AK,  AL,  AM,  AN,  AO,  AP,  AQ,  AR,  BK,  BL,  BM,  BN,  BO,  BP,  BQ,  BR,  CK,  CL,  CM,  CN,  CO,  CP,  CQ,  CR,  K,  L,  M,  N,  O,  P,  Q,  R
72Sus scrofaMutation(s): 0 
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase in E-state
Find proteins for Q4VT52 (Sus scrofa)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase membrane subunit 6.8PL Au, Bu, Cu, u42Sus scrofaMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
A, AA, AB, AC, B, BA, BB, BC, C, CA, CB, CC
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
ADP
Query on ADP
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AD, AF, BD, BF, CD, CF, D, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A, AA, AB, AC, AD, AF, B, BA, BB, BC, BD, BF, C, CA, CB, CC, CD, CF, D, F
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

View Full Validation Report


View more in-depth experimental data

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 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other