2F43

Rat liver F1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.306 
  • R-Value Observed: 0.306 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    2F43

  • 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, producing the high energy terminal bond of ATP ...

    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 U S A 95: 11065
    • 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
    • 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
    • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase alpha chain, mitochondrialA510Rattus norvegicusMutation(s): 0 
Gene Names: Atp5f1aAtp5a1
EC: 3.6.3.14
UniProt
Find proteins for P15999 (Rattus norvegicus)
Explore P15999 
Go to UniProtKB:  P15999
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase beta chain, mitochondrialB479Rattus norvegicusMutation(s): 0 
Gene Names: Atp5f1bAtp5b
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for P10719 (Rattus norvegicus)
Explore P10719 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase gamma chain, mitochondrialC [auth G]273Rattus norvegicusMutation(s): 0 
Gene Names: Atp5f1cAtp5cAtp5c1
EC: 3.6.3.14
UniProt
Find proteins for P35435 (Rattus norvegicus)
Explore P35435 
Go to UniProtKB:  P35435
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
H [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
VO4
Query on VO4

Download Ideal Coordinates CCD File 
F [auth B]VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.306 
  • R-Value Observed: 0.306 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.567α = 90
b = 144.567β = 90
c = 362.982γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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