4OD2

Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.248 

wwPDB Validation 3D Report Full Report



Literature

Structural and functional analysis of the interaction between the agonistic monoclonal antibody Apomab and the proapoptotic receptor DR5.

Adams, C.Totpal, K.Lawrence, D.Marsters, S.Pitti, R.Yee, S.Ross, S.Deforge, L.Koeppen, H.Sagolla, M.Compaan, D.Lowman, H.Hymowitz, S.Ashkenazi, A.

(2008) Cell Death Differ 15: 751-761

  • DOI: 10.1038/sj.cdd.4402306
  • Primary Citation of Related Structures:  
    4OD2

  • PubMed Abstract: 
  • Activation of the proapoptotic receptor death receptor5 (DR5) in various cancer cells triggers programmed cell death through the extrinsic pathway. We have generated a fully human monoclonal antibody (Apomab) that induces tumor cell apoptosis through ...

    Activation of the proapoptotic receptor death receptor5 (DR5) in various cancer cells triggers programmed cell death through the extrinsic pathway. We have generated a fully human monoclonal antibody (Apomab) that induces tumor cell apoptosis through DR5 and investigated the structural features of its interaction with DR5. Biochemical studies showed that Apomab binds DR5 tightly and selectively. X-ray crystallographic analysis of the complex between the Apomab Fab fragment and the DR5 ectodomain revealed an interaction epitope that partially overlaps with both regions of the Apo2 ligand/tumor necrosis factor-related apoptosis-inducing ligand binding site. Apomab induced DR5 clustering at the cell surface and stimulated a death-inducing signaling complex containing the adaptor molecule Fas-associated death domain and the apoptosis-initiating protease caspase-8. Fc crosslinking further augmented Apomab's proapoptotic activity. In vitro, Apomab triggered apoptosis in cancer cells, while sparing normal hepatocytes even upon anti-Fc crosslinking. In vivo, Apomab exerted potent antitumor activity as a single agent or in combination with chemotherapy in xenograft models, including those based on colorectal, non-small cell lung and pancreatic cancer cell lines. These results provide structural and functional insight into the interaction of Apomab with DR5 and support further investigation of this antibody for cancer therapy.


    Organizational Affiliation

    Department of Antibody Engineering, Genentech Inc., South San Francisco, CA 94080-4918, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fab fragment of drozitumab, light chainA213Homo sapiensMutation(s): 0 
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab fragment of drozitumab, heavy chainB232Homo sapiensMutation(s): 0 
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 10BS111Homo sapiensMutation(s): 0 
Gene Names: Death receptor 5DR5KILLERTNFRSF10BTRAILR2TRICK2UNQ160/PRO186ZTNFR9
Find proteins for O14763 (Homo sapiens)
Explore O14763 
Go to UniProtKB:  O14763
NIH Common Fund Data Resources
PHAROS  O14763
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.248 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.317α = 90
b = 128.317β = 90
c = 68.386γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release