2WPD

The Mg.ADP inhibited state of the yeast F1c10 ATP synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.432 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.286 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Mg.Adp-Inhibited State of the Yeast F1C10-ATP Synthase.

Dautant, A.Velours, J.Giraud, M.

(2010) J.Biol.Chem. 285: 29502

  • DOI: 10.1074/jbc.M110.124529
  • Also Cited By: 3ZRY

  • PubMed Abstract: 
  • The F(1)c(10) subcomplex of the yeast F(1)F(0)-ATP synthase includes the membrane rotor part c(10)-ring linked to a catalytic head, (αβ)(3), by a central stalk, γδε. The Saccharomyces cerevisiae yF(1)c(10)·ADP subcomplex was crystallized in the prese ...

    The F(1)c(10) subcomplex of the yeast F(1)F(0)-ATP synthase includes the membrane rotor part c(10)-ring linked to a catalytic head, (αβ)(3), by a central stalk, γδε. The Saccharomyces cerevisiae yF(1)c(10)·ADP subcomplex was crystallized in the presence of Mg·ADP, dicyclohexylcarbodiimide (DCCD), and azide. The structure was solved by molecular replacement using a high resolution model of the yeast F(1) and a bacterial c-ring model with 10 copies of the c-subunit. The structure refined to 3.43-Å resolution displays new features compared with the original yF(1)c(10) and with the yF(1) inhibited by adenylyl imidodiphosphate (AMP-PNP) (yF(1)(I-III)). An ADP molecule was bound in both β(DP) and β(TP) catalytic sites. The α(DP)-β(DP) pair is slightly open and resembles the novel conformation identified in yF(1), whereas the α(TP)-β(TP) pair is very closed and resembles more a DP pair. yF(1)c(10)·ADP provides a model of a new Mg·ADP-inhibited state of the yeast F(1). As for the original yF(1) and yF(1)c(10) structures, the foot of the central stalk is rotated by ∼40 ° with respect to bovine structures. The assembly of the F(1) central stalk with the F(0) c-ring rotor is mainly provided by electrostatic interactions. On the rotor ring, the essential cGlu(59) carboxylate group is surrounded by hydrophobic residues and is not involved in hydrogen bonding.


    Related Citations: 
    • Molecular Architecture of the Rotary Motor in ATP Synthase.
      Stock, D.,Leslie, A.G.W.,Walker, J.E.
      (1999) Science 286: 1700
    • Structure of the Rotor Ring of F-Type Na+-ATPase from Ilyobacter Tartaricus.
      Meier, T.,Polzer, P.,Diederichs, K.,Welte, W.,Dimroth, P.
      (2005) Science 308: 659
    • 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.W.,Mueller, D.M.
      (2009) J.Biol.Chem. 284: 10546
    • 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
    • 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.W.,Mueller, D.M.
      (2006) Embo J. 25: 5433


    Organizational Affiliation

    Université Bordeaux 2, CNRS, Institut de Biochimie et Génétique Cellulaires, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France. A.Dautant@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)Gene Names: ATP1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
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)Gene Names: ATP2
EC: 3.6.3.14
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
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)Gene Names: ATP3 (ATP3a, ATP3b)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
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)Gene Names: ATP16
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12165
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
I
61Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ATP15
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21306
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)Gene Names: OLI1 (ATP9, OLI3, PHO2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P61829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P61829
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
D, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-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: 3.432 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.286 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 134.990α = 90.00
b = 173.944β = 92.69
c = 137.016γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance