3ZRY

Rotor architecture in the F(1)-c(10)-ring complex of the yeast F-ATP synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.5 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.317 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Rotor Architecture in the Yeast and Bovine F(1)-C-Ring Complexes of F-ATP Synthase.

Giraud, M.-F.Paumard, P.Sanchez, C.Brethes, D.Velours, J.Dautant, A.

(2012) J.Struct.Biol. 177: 490

  • DOI: 10.1016/j.jsb.2011.10.015

  • PubMed Abstract: 
  • The F(1)F(O)-ATP synthase is a rotary molecular nanomotor. F(1) is a chemical motor driven by ATP hydrolysis while F(O) is an electrical motor driven by the proton flow. The two stepping motors are mechanically coupled through a common rotary shaft. ...

    The F(1)F(O)-ATP synthase is a rotary molecular nanomotor. F(1) is a chemical motor driven by ATP hydrolysis while F(O) is an electrical motor driven by the proton flow. The two stepping motors are mechanically coupled through a common rotary shaft. Up to now, the three available crystal structures of the F(1)c(10) sub-complex of the yeast F(1)F(O)-ATP synthase were isomorphous and then named yF(1)c(10)(I). In this crystal form, significant interactions of the c(10)-ring with the F(1)-head of neighboring molecules affected the overall conformation of the F(1)-c-ring complex. The symmetry axis of the F(1)-head and the inertia axis of the c-ring were tilted near the interface between the F(1)-central stalk and the c-ring rotor, resulting in an unbalanced machine. We have solved a new crystal form of the F(1)c(10) complex, named yF(1)c(10)(II), inhibited by adenylyl-imidodiphosphate (AMP-PNP) and dicyclohexylcarbodiimide (DCCD), at 6.5Å resolution in which the crystal packing has a weaker influence over the conformation of the F(1)-c-ring complex. yF(1)c(10)(II) provides a model of a more efficient generator. yF(1)c(10)(II) and bovine bF(1)c(8) structures share a common rotor architecture with the inertia center of the F(1)-stator close to the rotor axis.


    Related Citations: 
    • Crystal Structure of the Mgadp-Inhibited State of the Yeast F1C10-ATP Synthase.
      Dautant, A.,Velours, J.,Giraud, M.
      (2010) J.Biol.Chem. 285: 29502
    • Hydrogenated and Fluorinated Surfactants Derived from Tris(Hydroxymethyl)-Acrylamidomethane Allow the Purification of a Highly Active Yeast F1-F0 ATP-Synthase with an Enhanced Stability.
      Talbot, J.-C.,Dautant, A.,Polidori, A.,Pucci, B.,Cohen-Bouhacina, T.,Maali, A.,Salin, B.,Brethes, D.,Velours, J.,Giraud, M.-F.
      (2009) J.Bioenerg.Biomembr. 41: 349
    • Molecular Architecture of the Rotary Motor in ATP Synthase
      Stock, D.,Leslie, A.G.W.,Walker, J.E.
      (1999) Science 286: 1700
    • Novel Features of the Rotary Catalytic Mechanism Revealed in the Structure of Yeast F1 ATPase
      Kabaleeswaran, V.,Puri, N.,Walker, J.E.,Leslie, A.G.,Mueller, D.M.
      (2006) Embo J. 25: 5433


    Organizational Affiliation

    Univ. de Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France. marie-france.giraud@ibgc.cnrs.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
A, B, C
510Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATP1
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07251
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
D, E, F
478Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATP2
EC: 7.1.2.2
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00830
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
G
278Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATP3 (ATP3a, ATP3b)
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38077
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
H
138Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATP16
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12165
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE CATALYTIC SECTOR F1 EPSILON SUBUNIT
I
61Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for E9P9X4 (Saccharomyces cerevisiae)
Go to UniProtKB:  E9P9X4
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
J, K, L, M, N, O, P, Q, R, S
76Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: OLI1 (ATP9, OLI3, PHO2)
Find proteins for P61829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P61829
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C, D, F
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.5 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.317 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 107.690α = 90.00
b = 174.910β = 93.92
c = 164.260γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Other
  • Version 2.0: 2019-01-23
    Type: Advisory, Atomic model, Data collection, Other