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Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2A, monomer-masked refinement

Electron Microscopy
3.6Å resolution
PDB entry 6re0 coloured by chain, front view.
PDB entry 6re0 coloured by chain, side view.
PDB entry 6re0 coloured by chain, top view.
Source organism: Polytomella sp. Pringsheim 198.80
Assembly composition:
hetero 31-mer (preferred)
Entry contents: 18 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 31-mer
Accessible surface area: 254935.0 Å2
Buried surface area: 172421.19 Å2
Dissociation area: 2,204.2 Å2
Dissociation energy (ΔGdiss): 21.5 kcal/mol
Dissociation entropy (TΔSdiss): 12.92 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-100103

Macromolecules

ASA-10: Polytomella F-ATP synthase associated subunit 10
Chain: 0
Length: 82 amino acids
Theoretical weight: 8.73 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0A5H1ZR95 (Residues: 1-82; Coverage: 100%)
ASA-10: Polytomella F-ATP synthase associated subunit 10 in PDB entry 6re0, assembly 1, front view.
ASA-10: Polytomella F-ATP synthase associated subunit 10 in PDB entry 6re0, assembly 1, side view.
ASA-10: Polytomella F-ATP synthase associated subunit 10 in PDB entry 6re0, assembly 1, top view.
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ATP synthase associated protein ASA1
Chain: 1
Length: 618 amino acids
Theoretical weight: 68.68 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: Q85JD5 (Residues: 1-618; Coverage: 100%)
Gene name: asa1
ATP synthase associated protein ASA1 in PDB entry 6re0, assembly 1, front view.
ATP synthase associated protein ASA1 in PDB entry 6re0, assembly 1, side view.
ATP synthase associated protein ASA1 in PDB entry 6re0, assembly 1, top view.
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Mitochondrial ATP synthase subunit ASA2
Chain: 2
Length: 441 amino acids
Theoretical weight: 44.84 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D7P6B9 (Residues: 1-383; Coverage: 100%)
Mitochondrial ATP synthase subunit ASA2 in PDB entry 6re0, assembly 1, front view.
Mitochondrial ATP synthase subunit ASA2 in PDB entry 6re0, assembly 1, side view.
Mitochondrial ATP synthase subunit ASA2 in PDB entry 6re0, assembly 1, top view.
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Mitochondrial F1F0 ATP synthase associated 32 kDa protein
Chain: 3
Length: 325 amino acids
Theoretical weight: 34.85 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: K0J903 (Residues: 1-325; Coverage: 100%)
Gene name: asa3
Mitochondrial F1F0 ATP synthase associated 32 kDa protein in PDB entry 6re0, assembly 1, front view.
Mitochondrial F1F0 ATP synthase associated 32 kDa protein in PDB entry 6re0, assembly 1, side view.
Mitochondrial F1F0 ATP synthase associated 32 kDa protein in PDB entry 6re0, assembly 1, top view.
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Mitochondrial ATP synthase associated protein ASA4
Chain: 4
Length: 294 amino acids
Theoretical weight: 31.28 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D7NIZ2 (Residues: 1-294; Coverage: 100%)
Gene name: asa4
Mitochondrial ATP synthase associated protein ASA4 in PDB entry 6re0, assembly 1, front view.
Mitochondrial ATP synthase associated protein ASA4 in PDB entry 6re0, assembly 1, side view.
Mitochondrial ATP synthase associated protein ASA4 in PDB entry 6re0, assembly 1, top view.
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Mitochondrial F1F0 ATP synthase associated 14 kDa protein
Chain: 5
Length: 123 amino acids
Theoretical weight: 14 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0A024FSR7 (Residues: 1-123; Coverage: 100%)
Gene name: asa5
Mitochondrial F1F0 ATP synthase associated 14 kDa protein in PDB entry 6re0, assembly 1, front view.
Mitochondrial F1F0 ATP synthase associated 14 kDa protein in PDB entry 6re0, assembly 1, side view.
Mitochondrial F1F0 ATP synthase associated 14 kDa protein in PDB entry 6re0, assembly 1, top view.
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Mitochondrial ATP synthase subunit ASA6
Chain: 6
Length: 151 amino acids
Theoretical weight: 15.9 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D7P897 (Residues: 1-151; Coverage: 100%)
Mitochondrial ATP synthase subunit ASA6 in PDB entry 6re0, assembly 1, front view.
Mitochondrial ATP synthase subunit ASA6 in PDB entry 6re0, assembly 1, side view.
Mitochondrial ATP synthase subunit ASA6 in PDB entry 6re0, assembly 1, top view.
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Mitochondrial ATP synthase associated protein ASA7
Chain: 7
Length: 190 amino acids
Theoretical weight: 20.55 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D8V7I2 (Residues: 1-190; Coverage: 100%)
Mitochondrial ATP synthase associated protein ASA7 in PDB entry 6re0, assembly 1, front view.
Mitochondrial ATP synthase associated protein ASA7 in PDB entry 6re0, assembly 1, side view.
Mitochondrial ATP synthase associated protein ASA7 in PDB entry 6re0, assembly 1, top view.
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Mitochondrial ATP synthase subunit ASA8
Chain: 8
Length: 89 amino acids
Theoretical weight: 9.88 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D8V7I7 (Residues: 1-89; Coverage: 100%)
Mitochondrial ATP synthase subunit ASA8 in PDB entry 6re0, assembly 1, front view.
Mitochondrial ATP synthase subunit ASA8 in PDB entry 6re0, assembly 1, side view.
Mitochondrial ATP synthase subunit ASA8 in PDB entry 6re0, assembly 1, top view.
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ASA-9: Polytomella F-ATP synthase associated subunit 9
Chain: 9
Length: 97 amino acids
Theoretical weight: 11 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0A5H1ZR73 (Residues: 1-97; Coverage: 100%)
ASA-9: Polytomella F-ATP synthase associated subunit 9 in PDB entry 6re0, assembly 1, front view.
ASA-9: Polytomella F-ATP synthase associated subunit 9 in PDB entry 6re0, assembly 1, side view.
ASA-9: Polytomella F-ATP synthase associated subunit 9 in PDB entry 6re0, assembly 1, top view.
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V-ATPase proteolipid subunit C-like domain-containing protein
Chains: A, B, C, D, E, F, G, H, I, J
Length: 127 amino acids
Theoretical weight: 12.66 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D7P7X5 (Residues: 1-127; Coverage: 100%)
Pfam: ATP synthase subunit C
InterPro:
V-ATPase proteolipid subunit C-like domain-containing protein in PDB entry 6re0, assembly 1, front view.
V-ATPase proteolipid subunit C-like domain-containing protein in PDB entry 6re0, assembly 1, side view.
V-ATPase proteolipid subunit C-like domain-containing protein in PDB entry 6re0, assembly 1, top view.
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F-ATPase protein 6
Chain: M
Length: 327 amino acids
Theoretical weight: 34.8 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: H8PGG3 (Residues: 1-327; Coverage: 100%)
Gene name: atp6
Pfam: ATP synthase A chain
InterPro:
F-ATPase protein 6 in PDB entry 6re0, assembly 1, front view.
F-ATPase protein 6 in PDB entry 6re0, assembly 1, side view.
F-ATPase protein 6 in PDB entry 6re0, assembly 1, top view.
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Mitochondrial ATP synthase subunit OSCP
Chain: P
Length: 229 amino acids
Theoretical weight: 25.53 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D8V7I1 (Residues: 1-229; Coverage: 100%)
Pfam: ATP synthase delta (OSCP) subunit
InterPro:
Mitochondrial ATP synthase subunit OSCP in PDB entry 6re0, assembly 1, front view.
Mitochondrial ATP synthase subunit OSCP in PDB entry 6re0, assembly 1, side view.
Mitochondrial ATP synthase subunit OSCP in PDB entry 6re0, assembly 1, top view.
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epsilon: Polytomella F-ATP synthase epsilon subunit
Chain: Q
Length: 74 amino acids
Theoretical weight: 8.21 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0A5H1ZR74 (Residues: 1-74; Coverage: 100%)
Pfam: Mitochondrial ATP synthase epsilon chain
InterPro:
epsilon: Polytomella F-ATP synthase epsilon subunit in PDB entry 6re0, assembly 1, front view.
epsilon: Polytomella F-ATP synthase epsilon subunit in PDB entry 6re0, assembly 1, side view.
epsilon: Polytomella F-ATP synthase epsilon subunit in PDB entry 6re0, assembly 1, top view.
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ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein
Chain: R
Length: 199 amino acids
Theoretical weight: 20.88 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D7P7X6 (Residues: 1-199; Coverage: 100%)
Pfam: ATP synthase, Delta/Epsilon chain, beta-sandwich domain
InterPro:
ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein in PDB entry 6re0, assembly 1, front view.
ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein in PDB entry 6re0, assembly 1, side view.
ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein in PDB entry 6re0, assembly 1, top view.
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ATP synthase subunit gamma, mitochondrial
Chain: S
Length: 317 amino acids
Theoretical weight: 34.64 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: Q4LDE7 (Residues: 1-317; Coverage: 100%)
Gene name: atp3
Pfam: ATP synthase
InterPro:
ATP synthase gamma chain, mitochondrial in PDB entry 6re0, assembly 1, front view.
ATP synthase gamma chain, mitochondrial in PDB entry 6re0, assembly 1, side view.
ATP synthase gamma chain, mitochondrial in PDB entry 6re0, assembly 1, top view.
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ATP synthase subunit alpha
Chains: T, U, V
Length: 562 amino acids
Theoretical weight: 60.77 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0ZW40 (Residues: 1-562; Coverage: 100%)
Gene name: atp1
Pfam:
InterPro:
ATP synthase subunit alpha in PDB entry 6re0, assembly 1, front view.
ATP synthase subunit alpha in PDB entry 6re0, assembly 1, side view.
ATP synthase subunit alpha in PDB entry 6re0, assembly 1, top view.
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ATP synthase subunit beta
Chains: X, Y, Z
Length: 574 amino acids
Theoretical weight: 61.94 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0ZW41 (Residues: 1-574; Coverage: 100%)
Gene name: atp2
Pfam:
InterPro:
ATP synthase subunit beta in PDB entry 6re0, assembly 1, front view.
ATP synthase subunit beta in PDB entry 6re0, assembly 1, side view.
ATP synthase subunit beta in PDB entry 6re0, assembly 1, top view.
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