1MAB

RAT LIVER F1-ATPASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.290 
  • R-Value Work: 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.USA 95: 11065-11070

  • Also Cited By: 2F43

  • 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 ...

    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: 
    • 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
    • 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


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (F1-ATPASE ALPHA CHAIN)
A
510Rattus norvegicusGene Names: Atp5a1
Find proteins for P15999 (Rattus norvegicus)
Go to UniProtKB:  P15999
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (F1-ATPASE BETA CHAIN)
B
479Rattus norvegicusGene Names: Atp5b
EC: 3.6.3.14
Find proteins for P10719 (Rattus norvegicus)
Go to UniProtKB:  P10719
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (F1-ATPASE GAMMA CHAIN)
G
270Rattus norvegicusGene Names: Atp5c1 (Atp5c)
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

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.217 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 143.670α = 90.00
b = 143.670β = 90.00
c = 361.150γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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