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 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/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. 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE ALPHA CHAIN HEART ISOFORM
A, B, C
510Bos taurusMutation(s): 0 
UniProt
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UniProt GroupP19483
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE BETA CHAIN
D, E, F
482Bos taurusMutation(s): 0 
UniProt
Find proteins for P00829 (Bos taurus)
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UniProt GroupP00829
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE GAMMA CHAIN272Bos taurusMutation(s): 0 
UniProt
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UniProt GroupP05631
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE DELTA CHAIN146Bos taurusMutation(s): 0 
UniProt
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UniProt GroupP05630
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE EPSILON CHAIN50Bos taurusMutation(s): 0 
UniProt
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UniProt GroupP05632
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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J [auth A],
O [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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L [auth B],
Q [auth D],
U [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
DCW
Query on DCW

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S [auth D]DICYCLOHEXYLUREA
C13 H24 N2 O
ADFXKUOMJKEIND-UHFFFAOYSA-N
SO4
Query on SO4

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T [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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N [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

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K [auth A],
M [auth B],
P [auth C],
R [auth D],
V [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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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Ligand Structure Quality Assessment 


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
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Structure summary