7S11

Crystal structure of Fab in complex with mouse CD96 monomer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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This is version 1.2 of the entry. See complete history. 


Literature

Antibody blockade of CD96 by distinct molecular mechanisms.

Lee, P.S., Chau, B., Barman, I., Bee, C., Jashnani, A., Hogan, J.M., Aguilar, B., Dollinger, G., Rajpal, A., Strop, P.

(2021) MAbs 13: 1979800-1979800

  • DOI: https://doi.org/10.1080/19420862.2021.1979800
  • Primary Citation of Related Structures:  
    7S11, 7S13

  • PubMed Abstract: 

    The molecular interactions of mouse CD96 to CD155 ligand and to two surrogate antibodies have been investigated. Biophysical and structural studies demonstrate that CD96 forms a homodimer but assembles as 1:1 heterodimeric complexes with CD155 or with one of the surrogate antibodies, which compete for the same binding interface. In comparison, the other surrogate antibody binds across the mouse CD96 dimer and recognizes a quaternary epitope spanning both protomers to block exposure of the ligand-binding site. This study reveals different blocking mechanisms and modalities of these two antibodies and may provide insight into the functional effects of antibodies against CD96.

    • Organizational Affiliation: 

    Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface protein tactileA [auth C],
D,
G [auth E],
J [auth F]		122Mus musculusMutation(s): 0 
Gene Names: Cd96
UniProt & NIH Common Fund Data Resources
Find proteins for Q3U0X8 (Mus musculus)
Explore Q3U0X8 
Go to UniProtKB:  Q3U0X8
IMPC:  MGI:1934368
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3U0X8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainB [auth H],
E [auth I],
H [auth J],
K		229RattusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainC [auth L],
F [auth M],
I [auth N],
L [auth O]		216RattusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA		B [auth H],
E [auth I],
H [auth J],
K		L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.93α = 90
b = 154.89β = 90
c = 306γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description