4ZFF

Dual-acting Fab 5A12 in complex with VEGF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Deep Sequencing-guided Design of a High Affinity Dual Specificity Antibody to Target Two Angiogenic Factors in Neovascular Age-related Macular Degeneration.

Koenig, P.Lee, C.V.Sanowar, S.Wu, P.Stinson, J.Harris, S.F.Fuh, G.

(2015) J Biol Chem 290: 21773-21786

  • DOI: 10.1074/jbc.M115.662783
  • Primary Citation of Related Structures:  
    4ZFF, 4ZFG

  • PubMed Abstract: 
  • The development of dual targeting antibodies promises therapies with improved efficacy over mono-specific antibodies. Here, we engineered a Two-in-One VEGF/angiopoietin 2 antibody with dual action Fab (DAF) as a potential therapeutic for neovascular age-related macular degeneration ...

    The development of dual targeting antibodies promises therapies with improved efficacy over mono-specific antibodies. Here, we engineered a Two-in-One VEGF/angiopoietin 2 antibody with dual action Fab (DAF) as a potential therapeutic for neovascular age-related macular degeneration. Crystal structures of the VEGF/angiopoietin 2 DAF in complex with its two antigens showed highly overlapping binding sites. To achieve sufficient affinity of the DAF to block both angiogenic factors, we turned to deep mutational scanning in the complementarity determining regions (CDRs). By mutating all three CDRs of each antibody chain simultaneously, we were able not only to identify affinity improving single mutations but also mutation pairs from different CDRs that synergistically improve both binding functions. Furthermore, insights into the cooperativity between mutations allowed us to identify fold-stabilizing mutations in the CDRs. The data obtained from deep mutational scanning reveal that the majority of the 52 CDR residues are utilized differently for the two antigen binding function and permit, for the first time, the engineering of several DAF variants with sub-nanomolar affinity against two structurally unrelated antigens. The improved variants show similar blocking activity of receptor binding as the high affinity mono-specific antibodies against these two proteins, demonstrating the feasibility of generating a dual specificity binding surface with comparable properties to individual high affinity mono-specific antibodies.


    Organizational Affiliation

    From the Departments of Antibody Engineering, gml@gene.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fragment antigen binding (Fab) 5A12 Heavy chainA,
E [auth H]
228Homo sapiensMutation(s): 0 
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Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fragment antigen binding (Fab) 5A12 Light chainB,
F [auth L]
215Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Vascular endothelial growth factor AC, D99Homo sapiensMutation(s): 0 
Gene Names: VEGFAVEGF
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens)
Explore P15692 
Go to UniProtKB:  P15692
PHAROS:  P15692
GTEx:  ENSG00000112715 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15692
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth L]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.406α = 90
b = 313.892β = 90
c = 51.127γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2015-04-21 
  • Released Date: 2015-07-01 
  • Deposition Author(s): Harris, S.F., Wu, P.

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references