6T9E

Crystal structure of a bispecific DutaFab in complex with human PDGF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DutaFabs are engineered therapeutic Fab fragments that can bind two targets simultaneously.

Beckmann, R.Jensen, K.Fenn, S.Speck, J.Krause, K.Meier, A.Roth, M.Fauser, S.Kimbung, R.Logan, D.T.Steegmaier, M.Kettenberger, H.

(2021) Nat Commun 12: 708-708

  • DOI: https://doi.org/10.1038/s41467-021-20949-3
  • Primary Citation of Related Structures:  
    6T9D, 6T9E

  • PubMed Abstract: 

    We report the development of a platform of dual targeting Fab (DutaFab) molecules, which comprise two spatially separated and independent binding sites within the human antibody CDR loops: the so-called H-side paratope encompassing HCDR1, HCDR3 and LCDR2, and the L-side paratope encompassing LCDR1, LCDR3 and HCDR2. Both paratopes can be independently selected and combined into the desired bispecific DutaFabs in a modular manner. X-ray crystal structures illustrate that DutaFabs are able to bind two target molecules simultaneously at the same Fv region comprising a VH-VL heterodimer. In the present study, this platform is applied to generate DutaFabs specific for VEGFA and PDGF-BB, which show high affinities, physico-chemical stability and solubility, as well as superior efficacy over anti-VEGF monotherapy in vivo. These molecules exemplify the usefulness of DutaFabs as a distinct class of antibody therapeutics, which is currently being evaluated in patients.


  • Organizational Affiliation

    Roche Pharma Research and Early Development, Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany. pred.dutafabs@roche.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DutaFab mat VH chainA [auth AAA],
E [auth HHH]
220Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DutaFab mat VL chainB [auth BBB],
F [auth LLL]
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet-derived growth factor subunit BC [auth CCC],
D [auth DDD]
109Homo sapiensMutation(s): 0 
Gene Names: PDGFBPDGF2SIS
UniProt & NIH Common Fund Data Resources
Find proteins for P01127 (Homo sapiens)
Explore P01127 
Go to UniProtKB:  P01127
PHAROS:  P01127
GTEx:  ENSG00000100311 
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UniProt GroupP01127
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.301α = 90
b = 75.474β = 110.584
c = 116.505γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description