3FKS

Yeast F1 ATPase in the absence of bound nucleotides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Asymmetric structure of the yeast f1 ATPase in the absence of bound nucleotides.

Kabaleeswaran, V.Shen, H.Symersky, J.Walker, J.E.Leslie, A.G.Mueller, D.M.

(2009) J Biol Chem 284: 10546-10551

  • DOI: 10.1074/jbc.M900544200
  • Primary Citation of Related Structures:  
    3FKS

  • PubMed Abstract: 
  • The crystal structure of nucleotide-free yeast F(1) ATPase has been determined at a resolution of 3.6 A. The overall structure is very similar to that of the ground state enzyme. In particular, the beta(DP) and beta(TP) subunits both adopt the closed conformation found in the ground state structure despite the absence of bound nucleotides ...

    The crystal structure of nucleotide-free yeast F(1) ATPase has been determined at a resolution of 3.6 A. The overall structure is very similar to that of the ground state enzyme. In particular, the beta(DP) and beta(TP) subunits both adopt the closed conformation found in the ground state structure despite the absence of bound nucleotides. This implies that interactions between the gamma and beta subunits are as important as nucleotide occupancy in determining the conformational state of the beta subunits. Furthermore, this result suggests that for the mitochondrial enzyme, there is no state of nucleotide occupancy that would result in more than one of the beta subunits adopting the open conformation. The adenine-binding pocket of the beta(TP) subunit is disrupted in the apoenzyme, suggesting that the beta(DP) subunit is responsible for unisite catalytic activity.


    Organizational Affiliation

    Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, Illinois 60064, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit alpha, mitochondrial
A, B, C, J, K, L, S, T, U
A, B, C, J, K, L, S, T, U
510Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
UniProt
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP07251
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit beta, mitochondrial
D, E, F, M, N, O, V, W, X
D, E, F, M, N, O, V, W, X
484Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ATP2J2041YJR121W
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit gamma, mitochondrialG, P, Y278Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrialH, Q, Z138Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit epsilon, mitochondrialAA [auth 1],
I,
R
61Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
UniProt
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.934α = 90
b = 290.487β = 101.75
c = 188.7γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
X-GENdata reduction
X-GENdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description