1E79

Bovine F1-ATPase inhibited by DCCD (dicyclohexylcarbodiimide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Structure of the Central Stalk in Bovine F(1)-ATPase at 2.4 A Resolution.

Gibbons, C.Montgomery, M.G.Leslie, A.G.W.Walker, J.E.

(2000) Nat.Struct.Mol.Biol. 7: 1055

  • DOI: 10.1038/80981
  • Also Cited By: 1H8E, 1W0J, 1W0K, 2CK3

  • PubMed Abstract: 
  • The central stalk in ATP synthase, made of gamma, delta and epsilon subunits in the mitochondrial enzyme, is the key rotary element in the enzyme's catalytic mechanism. The gamma subunit penetrates the catalytic (alpha beta)(3) domain and protrudes b ...

    The central stalk in ATP synthase, made of gamma, delta and epsilon subunits in the mitochondrial enzyme, is the key rotary element in the enzyme's catalytic mechanism. The gamma subunit penetrates the catalytic (alpha beta)(3) domain and protrudes beneath it, interacting with a ring of c subunits in the membrane that drives rotation of the stalk during ATP synthesis. In other crystals of F(1)-ATPase, the protrusion was disordered, but with crystals of F(1)-ATPase inhibited with dicyclohexylcarbodiimide, the complete structure was revealed. The delta and epsilon subunits interact with a Rossmann fold in the gamma subunit, forming a foot. In ATP synthase, this foot interacts with the c-ring and couples the transmembrane proton motive force to catalysis in the (alpha beta)(3) domain.


    Related Citations: 
    • ATP Synthesis by Rotary Catalysis (Nobel Lecture)
      Walker, J.E.
      (1998) Angew.Chem.Int.Ed.Engl. 37: 2308
    • Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria
      Abrahams, J.P.,Leslie, A.G.W.,Lutter, R.,Walker, J.E.
      (1994) Nature 370: 621
    • Crystal Structure of the Epsilon Subunit of the Proton-Translocating ATP Synthase from Escherichia Coli
      Uhlin, U.,Cox, G.B.,Guss, J.M.
      (1997) Structure 9: 1219
    • Inactivation of Bovine Mitochondrial F1-ATPase with Dicyclohexyl-Carbodiimide [14C] Leads to the Modification of a Specific Glutamic-Acid Residue in the Beta Subunit
      Esch, F.S.,Bohlen, P.,Otsuka, A.S.,Yoshida, M.,Allison, W.S.
      (1981) J.Biol.Chem. 256: 9084
    • Molecular Architecture of the Rotary Motor in ATP Synthase
      Stock, D.,Leslie, A.G.W.,Walker, J.E.
      (1999) Science 286: 1700
    • Crystallization of F1-ATPase from Bovine Heart Mitochondria
      Lutter, R.,Abrahams, J.P.,Van Raaij, M.J.,Todd, R.J.,Lundqvist, T.,Buchanan, S.K.,Leslie, A.G.,Walker, J.E.
      (1993) J.Mol.Biol. 229: 787


    Organizational Affiliation

    The Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE ALPHA CHAIN HEART ISOFORM
A, B, C
510Bos taurusGene Names: ATP5A1 (ATP5A2)
Find proteins for P19483 (Bos taurus)
Go to Gene View: ATP5A1
Go to UniProtKB:  P19483
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE BETA CHAIN
D, E, F
482Bos taurusGene Names: ATP5B
EC: 3.6.3.14
Find proteins for P00829 (Bos taurus)
Go to Gene View: ATP5B
Go to UniProtKB:  P00829
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE GAMMA CHAIN
G
272Bos taurusGene Names: ATP5C1 (ATP5C)
Find proteins for P05631 (Bos taurus)
Go to Gene View: ATP5C1
Go to UniProtKB:  P05631
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE DELTA CHAIN
H
146Bos taurusGene Names: ATP5D
Find proteins for P05630 (Bos taurus)
Go to Gene View: ATP5D
Go to UniProtKB:  P05630
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE EPSILON CHAIN
I
50Bos taurusGene Names: ATP5E
Find proteins for P05632 (Bos taurus)
Go to Gene View: ATP5E
Go to UniProtKB:  P05632
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download SDF File 
Download CCD File 
D
DICYCLOHEXYLUREA
C13 H24 N2 O
ADFXKUOMJKEIND-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ADP
Query on ADP

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

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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: 2.4 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 267.200α = 90.00
b = 107.200β = 90.00
c = 135.900γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-03
    Type: Initial release
  • Version 1.1: 2011-08-31
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2012-11-28
    Type: Database references
  • Version 1.3: 2014-01-22
    Type: Database references