1MAB

RAT LIVER F1-ATPASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 11065-11070

  • DOI: 10.1073/pnas.95.19.11065
  • Primary Citation of Related Structures:  
    1MAB

  • PubMed Abstract: 
  • During mitochondrial ATP synthesis, F1-ATPase-the portion of the ATP synthase that contains the catalytic and regulatory nucleotide binding sites-undergoes a series of concerted conformational changes that couple proton translocation to the synthesis of the high levels of ATP required for cellular function ...

    During mitochondrial ATP synthesis, F1-ATPase-the portion of the ATP synthase that contains the catalytic and regulatory nucleotide binding sites-undergoes a series of concerted conformational changes that couple proton translocation to the synthesis of the high levels of ATP required for cellular function. In the structure of the rat liver F1-ATPase, determined to 2.8-A resolution in the presence of physiological concentrations of nucleotides, all three beta subunits contain bound nucleotide and adopt similar conformations. This structure provides the missing configuration of F1 necessary to define all intermediates in the reaction pathway. Incorporation of this structure suggests a mechanism of ATP synthesis/hydrolysis in which configurations of the enzyme with three bound nucleotides play an essential role.


    Related Citations: 
    • The Three-Dimensional Structure of Rat Liver Mitochondria F1-ATPase: X-Ray Diffraction Studies
      Bianchet, M.A., Medjahed, D., Hullihen, 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
    • Quaternary Structure of ATP Synthases: Symmetry and Asymmetry in the F1 Moiety
      Bianchet, M.A., Ysernhullihen, J., Pedersen, P.L., Amzel, L.M.
      (1991) J Biol Chem 266: 21197

    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA. mario@neruda.med.jhmi.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (F1-ATPASE ALPHA CHAIN)A510Rattus norvegicusMutation(s): 0 
Gene Names: Atp5f1aAtp5a1
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
PROTEIN (F1-ATPASE BETA CHAIN)B479Rattus norvegicusMutation(s): 0 
Gene Names: Atp5f1bAtp5b
EC: 7.1.2.2
UniProt
Find proteins for P10719 (Rattus norvegicus)
Explore P10719 
Go to UniProtKB:  P10719
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (F1-ATPASE GAMMA CHAIN)C [auth G]270Rattus norvegicusMutation(s): 0 
Gene Names: Atp5f1cAtp5cAtp5c1
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
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
Query on ADP

Download Ideal Coordinates CCD File 
G [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.67α = 90
b = 143.67β = 90
c = 361.15γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-09-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description