2JIZ

The Structure of F1-ATPase inhibited by resveratrol.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of Inhibition of Bovine F1-ATPase by Resveratrol and Related Polyphenols.

Gledhill, J.R.Montgomery, M.G.Leslie, A.G.W.Walker, J.E.

(2007) Proc Natl Acad Sci U S A 104: 13632

  • DOI: 10.1073/pnas.0706290104
  • Primary Citation of Related Structures:  
    2JIZ, 2JJ1, 2JJ2

  • PubMed Abstract: 
  • The structures of F(1)-ATPase from bovine heart mitochondria inhibited with the dietary phytopolyphenol, resveratrol, and with the related polyphenols quercetin and piceatannol have been determined at 2.3-, 2.4- and 2.7-A resolution, respectively. The inhibitors bind to a common site in the inside surface of an annulus made from loops in the three alpha- and three beta-subunits beneath the "crown" of beta-strands in their N-terminal domains ...

    The structures of F(1)-ATPase from bovine heart mitochondria inhibited with the dietary phytopolyphenol, resveratrol, and with the related polyphenols quercetin and piceatannol have been determined at 2.3-, 2.4- and 2.7-A resolution, respectively. The inhibitors bind to a common site in the inside surface of an annulus made from loops in the three alpha- and three beta-subunits beneath the "crown" of beta-strands in their N-terminal domains. This region of F(1)-ATPase forms a bearing to allow the rotation of the tip of the gamma-subunit inside the annulus during catalysis. The binding site is a hydrophobic pocket between the C-terminal tip of the gamma-subunit and the beta(TP) subunit, and the inhibitors are bound via H-bonds mostly to their hydroxyl moieties mediated by bound water molecules and by hydrophobic interactions. There are no equivalent sites between the gamma-subunit and either the beta(DP) or the beta(E) subunit. The inhibitors probably prevent both the synthetic and hydrolytic activities of the enzyme by blocking both senses of rotation of the gamma-subunit. The beneficial effects of dietary resveratrol may derive in part by preventing mitochondrial ATP synthesis in tumor cells, thereby inducing apoptosis.


    Organizational Affiliation

    Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORMA, B, C, H, I, J510Bos taurusMutation(s): 0 
Gene Names: ATP5F1AATP5A1ATP5A2
UniProt
Find proteins for P19483 (Bos taurus)
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Go to UniProtKB:  P19483
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT BETAD, E, F, K, L, M482Bos taurusMutation(s): 0 
Gene Names: ATP5F1BATP5B
EC: 7.1.2.2
UniProt
Find proteins for P00829 (Bos taurus)
Explore P00829 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE GAMMA CHAING, N272Bos taurusMutation(s): 0 
Gene Names: ATP5F1CATP5CATP5C1
UniProt
Find proteins for P05631 (Bos taurus)
Explore P05631 
Go to UniProtKB:  P05631
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
EA [auth F], HA [auth H], LA [auth I], O [auth A], OA [auth J], S [auth B], W [auth C], XA [auth M]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

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RA [auth K], Z [auth D]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
STL (Subject of Investigation/LOI)
Query on STL

Download Ideal Coordinates CCD File 
GA [auth G], ZA [auth N]RESVERATROL
C14 H12 O3
LUKBXSAWLPMMSZ-OWOJBTEDSA-N
 Ligand Interaction
PO4
Query on PO4

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DA [auth E], WA [auth L]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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CA [auth D] , JA [auth H] , KA [auth H] , NA [auth I] , Q [auth A] , QA [auth J] , R [auth A] , U [auth B] , 
CA [auth D], JA [auth H], KA [auth H], NA [auth I], Q [auth A], QA [auth J], R [auth A], U [auth B], UA [auth K], V [auth B], VA [auth K], Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

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BA [auth D], TA [auth K]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA [auth D] , FA [auth F] , IA [auth H] , MA [auth I] , P [auth A] , PA [auth J] , SA [auth K] , T [auth B] , 
AA [auth D], FA [auth F], IA [auth H], MA [auth I], P [auth A], PA [auth J], SA [auth K], T [auth B], X [auth C], YA [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.776α = 90
b = 277.368β = 90.19
c = 137.827γ = 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: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance