3FKS | pdb_00003fks

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 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 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 Biological Chem 284: 10546-10551

  • DOI: https://doi.org/10.1074/jbc.M900544200
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 1,120.1 kDa 
  • Atom Count: 71,793 
  • Modeled Residue Count: 9,507 
  • Deposited Residue Count: 10,377 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha, mitochondrial
A, B, C, J, K
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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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit beta, mitochondrial
D, E, F, M, N
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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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit gamma, mitochondrial
G, P, Y
278Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
UniProt
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrial
H, Q, Z
138Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
UniProt
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence 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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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
BA [auth A]
CA [auth B]
DA [auth C]
EA [auth D]
FA [auth F]
BA [auth A],
CA [auth B],
DA [auth C],
EA [auth D],
FA [auth F],
GA [auth J],
HA [auth K],
IA [auth L],
JA [auth M],
KA [auth N],
LA [auth O],
MA [auth S],
NA [auth T],
OA [auth U],
PA [auth X]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free:  0.306 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
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
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description