2AP2

SINGLE CHAIN FV OF C219 IN COMPLEX WITH SYNTHETIC EPITOPE PEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Antibody C219 recognizes an alpha-helical epitope on P-glycoprotein.

van Den Elsen, J.M.Kuntz, D.A.Hoedemaeker, F.J.Rose, D.R.

(1999) Proc Natl Acad Sci U S A 96: 13679-13684

  • DOI: https://doi.org/10.1073/pnas.96.24.13679
  • Primary Citation of Related Structures:  
    2AP2

  • PubMed Abstract: 

    The ABC transporter, P-glycoprotein, is an integral membrane protein that mediates the ATP-driven efflux of drugs from multidrug-resistant cancer and HIV-infected cells. Anti-P-glycoprotein antibody C219 binds to both of the ATP-binding regions of P-glycoprotein and has been shown to inhibit its ATPase activity and drug binding capacity. C219 has been widely used in a clinical setting as a tumor marker, but recent observations of cross-reactivity with other proteins, including the c-erbB2 protein in breast cancer cells, impose potential limitations in detecting P-glycoprotein. We have determined the crystal structure at a resolution of 2.4 A of the variable fragment of C219 in complex with an epitope peptide derived from the nucleotide binding domain of P-glycoprotein. The 14-residue peptide adopts an amphipathic alpha-helical conformation, a secondary structure not previously observed in structures of antibody-peptide complexes. Together with available biochemical data, the crystal structure of the C219-peptide complex indicates the molecular basis of the cross-reactivity of C219 with non-multidrug resistance-associated proteins. Alignment of the C219 epitope with the recent crystal structure of the ATP-binding subunit of histidine permease suggests a structural basis for the inhibition of the ATP and drug binding capacity of P-glycoprotein by C219. The results provide a rationale for the development of C219 mutants with improved specificity and affinity that could be useful in antibody-based P-glycoprotein detection and therapy in multidrug resistant cancers.


  • Organizational Affiliation

    Ontario Cancer Institute, Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto M5G 2M9, Ontario, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SINGLE CHAIN FVA,
B [auth C]
271Mus musculusMutation(s): 0 
UniProt
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Go to UniProtKB:  Q6KB05
Find proteins for Q505N9 (Mus musculus)
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Go to UniProtKB:  Q505N9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ505N9Q6KB05
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
P-GLYCOPROTEINC [auth P],
D [auth Q]
14Cricetulus griseusMutation(s): 0 
UniProt
Find proteins for P21448 (Cricetulus griseus)
Explore P21448 
Go to UniProtKB:  P21448
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21448
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.792α = 90
b = 82.659β = 90
c = 93.978γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-24
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-03-07
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-11-13
    Changes: Database references, Derived calculations
  • Version 2.2: 2023-08-23
    Changes: Data collection, Database references, Refinement description