1MOE

The three-dimensional structure of an engineered scFv T84.66 dimer or diabody in VL to VH linkage.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Crystal Structure of an Anti-CEA scFv Diabody Assembled from T84.66 scFvs in VL-to-VH Orientation: Implications for Diabody Flexibility

Carmichael, J.A.Power, B.E.Garrett, T.P.Yazaki, P.J.Shively, J.E.Raubischek, A.A.Wu, A.M.Hudson, P.J.

(2003) J Mol Biol 326: 341-351

  • DOI: 10.1016/s0022-2836(02)01428-6
  • Primary Citation of Related Structures:  
    1MOE

  • PubMed Abstract: 
  • Diabodies (scFv dimers) are small, bivalent antibody mimetics of approximately 55kDa in size that possess rapid in vivo targeting pharmacokinetics compared to the intact parent antibody, and may prove highly suitable for imaging and therapeutic applications ...

    Diabodies (scFv dimers) are small, bivalent antibody mimetics of approximately 55kDa in size that possess rapid in vivo targeting pharmacokinetics compared to the intact parent antibody, and may prove highly suitable for imaging and therapeutic applications. Here, we describe T84.66Di, the first diabody crystal structure in which the scFvs comprise V domains linked in the V(L)-to-V(H) orientation. The structure was determined by X-ray diffraction analysis to 2.6 A resolution. The T84.66Di scFv was constructed from the anti-carcinoembryonic antigen (anti-CEA) antibody T84.66 variable domains connected by an eight residue peptide linker to provide flexibility between Fv modules and promote dimer formation with bivalent affinity to the cell-surface target, CEA. Therefore, it was surprising to observe a close association of some Fv module complementarity-determining regions in the T84.66 diabody crystal, especially compared to other diabody structures all of which are linked in the opposite V(H)-to-V(L) orientation. The differences between the arrangement of Fv modules in the T84.66Di V(L)-to-V(H) linked diabody structure compared to the crystal structure of L5MK16 and other proposed V(H)-to-V(L) linked diabodies has been investigated and their potential for flexibility discussed. The comparison between V(H)-to-V(L) and V(L)-to-V(H) linked diabodies revealed in this study represents a limited repertoire of possible diabody Fv orientations, but one that reveals the potential flexibility of these molecules. This analysis therefore provides some signposts that may impact on future molecular designs for these therapeutic molecules with respect to diabody flexibility and avidity.


    Related Citations: 
    • Mammalian expression and hollow fiber bioreactor production of recombinant anti-CEA diabody and minibody for clinical applications.
      Yazaki, P.J., Shively, L., Clark, C., Cheung, C.W., Le, W., Szpikowska, B., Shively, J.E., Raubitschek, A.A., Wu, A.M.
      (2001) J Immunol Methods 253: 195
    • Structure of an Exoglucanase complexed with conduritol B epoxide from A 50um Crystal using monocappilary optics.
      Varghese, L.N., Van Donkelaar, A., Hrmova, M., Fincher, G.A., Baliac, D.X., Barnia, Z.
      (1999) Acta Crystallogr A 55: 329

    Organizational Affiliation

    CSIRO Health Sciences and Nutrition, 343 Royal Parade, Parkville 3052, Vic., Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
anti-CEA mAb T84.66A, B240Mus musculusMutation(s): 0 
UniProt
Find proteins for Q5R3X1 (Mus musculus)
Explore Q5R3X1 
Go to UniProtKB:  Q5R3X1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5R3X1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B],
E [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.243 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.314α = 90
b = 64.314β = 90
c = 247.93γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2017-10-11
    Changes: Refinement description