1KMH | pdb_00001kmh

Crystal Structure of spinach chloroplast F1-ATPase complexed with tentoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.319 (Depositor) 
  • R-Value Work: 
    0.297 (Depositor) 
  • R-Value Observed: 
    0.298 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Structure of spinach chloroplast F1-ATPase complexed with the phytopathogenic inhibitor tentoxin.

Groth, G.

(2002) Proc Natl Acad Sci U S A 99: 3464-3468

  • DOI: https://doi.org/10.1073/pnas.052546099
  • Primary Citation Related Structures: 
    1KMH

  • PubMed Abstract: 

    Tentoxin, a natural cyclic tetrapeptide produced by phytopathogenic fungi from the Alternaria species affects the catalytic function of the chloroplast F(1)-ATPase in certain sensitive species of plants. In this study, we show that the uncompetitive inhibitor tentoxin binds to the alphabeta-interface of the chloroplast F(1)-ATPase in a cleft localized at betaAsp-83. Most of the binding site is located on the noncatalytic alpha-subunit. The crystal structure of the tentoxin-inhibited CF(1)-complex suggests that the inhibitor is hydrogen bonded to Asp-83 in the catalytic beta-subunit but forms hydrophobic contacts with residues Ile-63, Leu-65, Val-75, Tyr-237, Leu-238, and Met-274 in the adjacent alpha-subunit. Except for minor changes around the tentoxin-binding site, the structure of the chloroplast alpha(3)beta(3)-core complex is the same as that determined with the native chloroplast ATPase. Tentoxin seems to act by inhibiting inter-subunit contacts at the alphabeta-interface and by blocking the interconversion of binding sites in the catalytic mechanism.


  • Organizational Affiliation
    • Heinrich-Heine-Universität, Biochemie der Pflanzen, Universitätsstrasse 1, D-40225 Duesseldorf, Germany. georg.groth@uni-duesseldorf.de

Macromolecule Content 

  • Total Structure Weight: 109.84 kDa 
  • Atom Count: 7,217 
  • Modeled Residue Count: 944 
  • Deposited Residue Count: 1,005 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPase alpha subunit507Spinacia oleraceaMutation(s): 0 
EC: 7.1.2.2
UniProt
Find proteins for P06450 (Spinacia oleracea)
Explore P06450 
Go to UniProtKB:  P06450
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06450
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPase beta subunit498Spinacia oleraceaMutation(s): 0 
EC: 7.1.2.2
UniProt
Find proteins for P00825 (Spinacia oleracea)
Explore P00825 
Go to UniProtKB:  P00825
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00825
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TTX

Query on TTX



Download:Ideal Coordinates CCD File
C [auth B]TENTOXIN
C22 H30 N4 O4
SIIRBDOFKDACOK-LFXZBHHUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.319 (Depositor) 
  • R-Value Work:  0.297 (Depositor) 
  • R-Value Observed: 0.298 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.887α = 90
b = 146.887β = 90
c = 381.679γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
DENZOdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2002-03-13 
  • Deposition Author(s): Groth, G.

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2024-12-25
    Changes: Advisory, Derived calculations, Structure summary