1E79

Bovine F1-ATPase inhibited by DCCD (dicyclohexylcarbodiimide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 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 Biol 7: 1055

  • DOI: 10.1038/80981
  • Primary Citation of Related Structures:  
    1E79

  • 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 beneath it, interacting with a ring of c subunits in the membrane that drives rotation of the stalk during ATP synthesis ...

    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: 
    • Molecular Architecture of the Rotary Motor in ATP Synthase
      Stock, D., Leslie, A.G.W., Walker, J.E.
      (1999) Science 286: 1700
    • ATP Synthesis by Rotary Catalysis (Nobel Lecture)
      Walker, J.E.
      (1998) Angew Chem Int Ed Engl 37: 2308
    • 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
    • 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
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE ALPHA CHAIN HEART ISOFORMA, B, C510Bos taurusMutation(s): 0 
Gene Names: ATP5F1AATP5A1ATP5A2
UniProt
Find proteins for P19483 (Bos taurus)
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE BETA CHAIND, E, F482Bos taurusMutation(s): 0 
Gene Names: ATP5F1BATP5B
EC: 7.1.2.2
UniProt
Find proteins for P00829 (Bos taurus)
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE GAMMA CHAING272Bos taurusMutation(s): 0 
Gene Names: ATP5F1CATP5CATP5C1
UniProt
Find proteins for P05631 (Bos taurus)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE DELTA CHAINH146Bos taurusMutation(s): 0 
Gene Names: ATP5F1DATP5D
UniProt
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE EPSILON CHAINI50Bos taurusMutation(s): 0 
Gene Names: ATP5F1EATP5E
UniProt
Find proteins for P05632 (Bos taurus)
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
J [auth A], O [auth C]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
L [auth B], Q [auth D], U [auth F]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
DCW
Query on DCW

Download Ideal Coordinates CCD File 
S [auth D]DICYCLOHEXYLUREA
C13 H24 N2 O
ADFXKUOMJKEIND-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
T [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
N [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth A], M [auth B], P [auth C], R [auth D], V [auth F]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 267.2α = 90
b = 107.2β = 90
c = 135.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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