2F43

Rat liver F1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.306 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mitochondrial ATP synthase: Crystal structure of the catalytic F1 unit in a vanadate-induced transition-like state and implications for mechanism.

Chen, C.Saxena, A.K.Simcoke, W.N.Garboczi, D.N.Pedersen, P.L.Ko, Y.H.

(2006) J.Biol.Chem. 281: 13777-13783

  • DOI: 10.1074/jbc.M513369200

  • PubMed Abstract: 
  • ATP synthesis from ADP, P(i), and Mg2+ takes place in mitochondria on the catalytic F1 unit (alpha3beta3gammedeltaepsilon) of the ATP synthase complex (F0F1), a remarkable nanomachine that interconverts electrochemical and mechanical energy, producin ...

    ATP synthesis from ADP, P(i), and Mg2+ takes place in mitochondria on the catalytic F1 unit (alpha3beta3gammedeltaepsilon) of the ATP synthase complex (F0F1), a remarkable nanomachine that interconverts electrochemical and mechanical energy, producing the high energy terminal bond of ATP. In currently available structural models of F1, the P-loop (amino acid residues 156GGAGVGKT163) contributes to substrate binding at the subunit catalytic sites. Here, we report the first transition state-like structure of F1 (ADP.V(i).Mg.F1) from rat liver that was crystallized with the phosphate (P(i)) analog vanadate (VO(3-)4 or V(i)). Compared with earlier "ground state" structures, this new F1 structure reveals that the active site region has undergone significant remodeling. P-loop residue alanine 158 is located much closer to V(i) than it is to P(i) in a previous structural model. No significant movements of P-loop residues of the subunit were observed at its analogous but noncatalytic sites. Under physiological conditions, such active site remodeling involving the small hydrophobic alanine residue may promote ATP synthesis by lowering the local dielectric constant, thus facilitating the dehydration of ADP and P(i). This new crystallographic study provides strong support for the catalytic mechanism of ATP synthesis deduced from earlier biochemical studies of liver F1 conducted in the presence of V(i) (Ko, Y. H., Bianchet, M., Amzel, L. M., and Pedersen, P. L. (1997) J. Biol. Chem. 272, 18875-18881; Ko, Y. H., Hong, S., and Pedersen, P. L. (1999) J. Biol. Chem. 274, 28853-28856).


    Related Citations: 
    • The 2.8-A structure of rat liver F1-ATPase: configuration of a critical intermediate in ATP synthesis/hydrolysis.
      Bianchet, M.A.,Hullihen, J.,Pedersen, P.L.,Amzel, L.M.
      (1998) Proc.Natl.Acad.Sci.Usa 95: 11065
    • Quaternary structure of ATP synthases: symmetry and asymmetry in the F1 moiety.
      Amzel, L.M.,Bianchet, M.A.,Pedersen, P.L.
      (1992) J.Bioenerg.Biomembr. 24: 429
    • The three-dimensional structure of rat liver mitochodria F1-ATPase: X-ray diffraction studies.
      Bianchet, M.,Medjahed, D.,Hulihen, J.,Pedersen, P.L.,Amzel, L.M.
      (1994) Biochim.Biophys.Acta 1187: 163
    • Mitochondrial ATP synthase. Quaternary structure of the F1 moiety at 3.6 A determined by x-ray diffraction analysis.
      Bianchet, M.,Ysern, X.,Hullihen, J.,Pedersen, P.L.,Amzel, L.M.
      (1991) J.Biol.Chem. 266: 21197


    Organizational Affiliation

    Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase alpha chain, mitochondrial
A
510Rattus norvegicusMutation(s): 0 
Gene Names: Atp5f1a (Atp5a1)
Find proteins for P15999 (Rattus norvegicus)
Go to UniProtKB:  P15999
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase beta chain, mitochondrial
B
479Rattus norvegicusMutation(s): 0 
Gene Names: Atp5f1b (Atp5b)
EC: 7.1.2.2
Find proteins for P10719 (Rattus norvegicus)
Go to UniProtKB:  P10719
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase gamma chain, mitochondrial
G
273Rattus norvegicusMutation(s): 0 
Gene Names: Atp5f1c (Atp5c, Atp5c1)
Find proteins for P35435 (Rattus norvegicus)
Go to UniProtKB:  P35435
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

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Download CCD File 
B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
VO4
Query on VO4

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Download CCD File 
B
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.306 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 144.567α = 90.00
b = 144.567β = 90.00
c = 362.982γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
CCP4data scaling
MOLREPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance