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Structure of the human ATP synthase bound to bedaquiline (membrane domain)

Electron Microscopy
3.13Å resolution
PDB entry 8khf coloured by chain, front view.
PDB entry 8khf coloured by chain, side view.
PDB entry 8khf coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero nonadecamer (preferred)
Entry contents: 12 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: ATP synthase
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Multimeric state: hetero nonadecamer
Accessible surface area: 62508.73 Å2
Buried surface area: 57123.46 Å2
Dissociation area: 1,214.72 Å2
Dissociation energy (ΔGdiss): -8.6 kcal/mol
Dissociation entropy (TΔSdiss): 14.53 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-271869

Macromolecules

ATP synthase F(0) complex subunit C1, mitochondrial
Chains: 1, 2, 3, 4, 5, 6, 7, 8
Length: 75 amino acids
Theoretical weight: 7.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P05496 (Residues: 62-136; Coverage: 55%)
Gene names: ATP5G1, ATP5MC1
Pfam: ATP synthase subunit C
ATP synthase F(0) complex subunit C1, mitochondrial in PDB entry 8khf, assembly 1, front view.
ATP synthase F(0) complex subunit C1, mitochondrial in PDB entry 8khf, assembly 1, side view.
ATP synthase F(0) complex subunit C1, mitochondrial in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P05496  
17510203040506070
 
204060DIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM
UniProt
P05496
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ATP synthase F(1) complex subunit gamma, mitochondrial
Chain: G
Length: 273 amino acids
Theoretical weight: 30.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P36542 (Residues: 26-298; Coverage: 92%)
Gene names: ATP5C, ATP5C1, ATP5CL1, ATP5F1C
Pfam: ATP synthase
ATP synthase subunit gamma, mitochondrial in PDB entry 8khf, assembly 1, front view.
ATP synthase subunit gamma, mitochondrial in PDB entry 8khf, assembly 1, side view.
ATP synthase subunit gamma, mitochondrial in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P36542  
127320406080100120140160180200220240260
 
100200
UniProt
P36542
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ATP synthase F(1) complex subunit delta, mitochondrial
Chain: H
Length: 146 amino acids
Theoretical weight: 15.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P30049 (Residues: 23-168; Coverage: 87%)
Gene names: ATP5D, ATP5F1D
Pfam:
ATP synthase subunit delta, mitochondrial in PDB entry 8khf, assembly 1, front view.
ATP synthase subunit delta, mitochondrial in PDB entry 8khf, assembly 1, side view.
ATP synthase subunit delta, mitochondrial in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P30049  
114620406080100120140
 
50100
UniProt
P30049
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ATP synthase F(1) complex subunit epsilon, mitochondrial
Chain: I
Length: 51 amino acids
Theoretical weight: 5.79 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P56381 (Residues: 1-51; Coverage: 100%)
Gene names: ATP5E, ATP5F1E
Pfam: Mitochondrial ATP synthase epsilon chain
ATP synthase subunit epsilon, mitochondrial in PDB entry 8khf, assembly 1, front view.
ATP synthase subunit epsilon, mitochondrial in PDB entry 8khf, assembly 1, side view.
ATP synthase subunit epsilon, mitochondrial in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P56381  
1515101520253035404550
 
2040MVAYWRQAGLSYIRYSQICAKAVRDALKTEFKANAEKTSGSNVKIVKVKKE
UniProt
P56381
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ATP synthase peripheral stalk subunit b, mitochondrial
Chain: K
Length: 214 amino acids
Theoretical weight: 24.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P24539 (Residues: 43-256; Coverage: 84%)
Gene names: ATP5F1, ATP5PB
Pfam: Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
ATP synthase F(0) complex subunit B1, mitochondrial in PDB entry 8khf, assembly 1, front view.
ATP synthase F(0) complex subunit B1, mitochondrial in PDB entry 8khf, assembly 1, side view.
ATP synthase F(0) complex subunit B1, mitochondrial in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P24539  
121420406080100120140160180200
 
100200
UniProt
P24539
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ATP synthase peripheral stalk subunit d, mitochondrial
Chain: M
Length: 160 amino acids
Theoretical weight: 18.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75947 (Residues: 2-161; Coverage: 99%)
Gene names: ATP5H, ATP5PD, My032
Pfam: ATP synthase D chain, mitochondrial (ATP5H)
ATP synthase subunit d, mitochondrial in PDB entry 8khf, assembly 1, front view.
ATP synthase subunit d, mitochondrial in PDB entry 8khf, assembly 1, side view.
ATP synthase subunit d, mitochondrial in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: O75947  
116020406080100120140160
 
50100150
UniProt
O75947
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ATP synthase F(0) complex subunit a
Chain: N
Length: 226 amino acids
Theoretical weight: 24.83 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00846 (Residues: 1-226; Coverage: 100%)
Gene names: ATP6, ATPASE6, MT-ATP6, MTATP6
Pfam: ATP synthase A chain
ATP synthase subunit a in PDB entry 8khf, assembly 1, front view.
ATP synthase subunit a in PDB entry 8khf, assembly 1, side view.
ATP synthase subunit a in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P00846  
122620406080100120140160180200220
 
100200
UniProt
P00846
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ATP synthase F(0) complex subunit j, mitochondrial
Chain: P
Length: 58 amino acids
Theoretical weight: 6.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P56378 (Residues: 1-58; Coverage: 100%)
Gene names: ATP5MJ, ATP5MPL, C14orf2, MP68, PRO1574
Pfam: Mitochondrial proteolipid
ATP synthase subunit ATP5MJ, mitochondrial in PDB entry 8khf, assembly 1, front view.
ATP synthase subunit ATP5MJ, mitochondrial in PDB entry 8khf, assembly 1, side view.
ATP synthase subunit ATP5MJ, mitochondrial in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P56378  
158510152025303540455055
 
2040MLQSIIKNIWIPMKPYYTKVYQEIWIGMGLMGFIVYKIRAADKRSKALKASAPAPGHH
UniProt
P56378
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ATP synthase F(0) complex subunit 8
Chain: Q
Length: 68 amino acids
Theoretical weight: 8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P03928 (Residues: 1-68; Coverage: 100%)
Gene names: ATP8, ATPASE8, MT-ATP8, MTATP8
Pfam: ATP synthase protein 8
ATP synthase protein 8 in PDB entry 8khf, assembly 1, front view.
ATP synthase protein 8 in PDB entry 8khf, assembly 1, side view.
ATP synthase protein 8 in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P03928  
1685101520253035404550556065
 
204060MPQLNTTVWPTMITPMLLTLFLITQLKMLNTNYHLPPSPKPMKMKNYNKPWEPKWTKICSLHSLPPQS
UniProt
P03928
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ATP synthase F(0) complex subunit f, mitochondrial
Chain: R
Length: 93 amino acids
Theoretical weight: 10.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P56134 (Residues: 2-94; Coverage: 99%)
Gene names: ATP5J2, ATP5JL, ATP5MF
Pfam: Mitochondrial F1F0-ATP synthase, subunit f
ATP synthase subunit f, mitochondrial in PDB entry 8khf, assembly 1, front view.
ATP synthase subunit f, mitochondrial in PDB entry 8khf, assembly 1, side view.
ATP synthase subunit f, mitochondrial in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P56134  
193102030405060708090
 
20406080ASVGECPAPVPVKDKKLLEVKLGELPSWILMRDFSPSGIFGAFQRGYYRYYNKYINVKKGSISGITMVLACYVLFSYSFSYKHLKHERLRKYH
UniProt
P56134
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ATP synthase F(0) complex subunit g, mitochondrial
Chain: S
Length: 102 amino acids
Theoretical weight: 11.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75964 (Residues: 2-103; Coverage: 99%)
Gene names: ATP5L, ATP5MG
Pfam: Mitochondrial ATP synthase g subunit
ATP synthase subunit g, mitochondrial in PDB entry 8khf, assembly 1, front view.
ATP synthase subunit g, mitochondrial in PDB entry 8khf, assembly 1, side view.
ATP synthase subunit g, mitochondrial in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: O75964  
1102102030405060708090100
 
50100AQFVRNLVEKTPALVNAAVTYSKPRLATFWYYAKVELVPPTPAEIPRAIQSLKKIVNSAQTGSFKQLTVKEAVLNGLVATEVLMWFYVGEIIGKRGIIGYDV
UniProt
O75964
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ATP synthase F(0) complex subunit e, mitochondrial
Chain: T
Length: 69 amino acids
Theoretical weight: 7.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P56385 (Residues: 1-69; Coverage: 100%)
Gene names: ATP5I, ATP5K, ATP5ME
Pfam: ATP synthase E chain
ATP synthase subunit e, mitochondrial in PDB entry 8khf, assembly 1, front view.
ATP synthase subunit e, mitochondrial in PDB entry 8khf, assembly 1, side view.
ATP synthase subunit e, mitochondrial in PDB entry 8khf, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P56385  
1695101520253035404550556065
 
204060MVPPVQVSPLIKLGRYSALFLGVAYGATRYNYLKPRAEEERRIAAEEKKKQDELKRIARELAEDDSILK
UniProt
P56385
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