8RP8

Structure of K2 Fab in complex with human CD47 ECD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


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Literature

Structural analysis of light chain-driven bispecific antibodies targeting CD47 and PD-L1.

Malinge, P.Chauchet, X.Bourguignon, J.Bosson, N.Calloud, S.Bautzova, T.Borlet, M.Laursen, M.Kelpsas, V.Rose, N.Gueneau, F.Ravn, U.Magistrelli, G.Fischer, N.

(2024) MAbs 16: 2362432-2362432

  • DOI: https://doi.org/10.1080/19420862.2024.2362432
  • Primary Citation of Related Structures:  
    8RP8, 8RPB

  • PubMed Abstract: 

    In contrast to natural antibodies that rely mainly on the heavy chain to establish contacts with their cognate antigen, we have developed a bispecific antibody format in which the light chain (LC) drives antigen binding and specificity. To better understand epitope-paratope interactions in this context, we determined the X-ray crystallographic structures of an antigen binding fragment (Fab) in complex with human CD47 and another Fab in complex with human PD-L1. These Fabs contain a κ-LC and a λ-LC, respectively, which are paired with an identical heavy chain (HC). The structural analysis of these complexes revealed the dominant contribution of the LCs to antigen binding, but also that the common HC provides some contacts in both CD47 and PD-L1 Fab complexes. The anti-CD47 Fab was affinity optimized by diversifying complementary-determining regions of the LC followed by phage display selections. Using homology modeling, the contributions of the amino acid modification to the affinity increase were analyzed. Our results demonstrate that, despite a less prominent role in natural antibodies, the LC can mediate high affinity binding to different antigens and neutralize their biological function. Importantly, Fabs containing a common variable heavy (VH) domain enable the generation of bispecific antibodies retaining a truly native structure, maximizing their therapeutic potential.


  • Organizational Affiliation

    Light Chain Bioscience - Novimmune SA, Plan-les-Ouates, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
K2 Fab heavy chainA,
E [auth H]
223Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
K2 Fab light chainB,
F [auth L]
215Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Leukocyte surface antigen CD47
C, D
129Homo sapiensMutation(s): 0 
Gene Names: CD47MER6
UniProt & NIH Common Fund Data Resources
Find proteins for Q08722 (Homo sapiens)
Explore Q08722 
Go to UniProtKB:  Q08722
PHAROS:  Q08722
GTEx:  ENSG00000196776 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08722
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth C]
J [auth C]
K [auth C]
L [auth D]
M [auth D]
I [auth C],
J [auth C],
K [auth C],
L [auth D],
M [auth D],
N [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A],
O [auth H]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B],
P [auth L]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
C, D
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.415α = 109.45
b = 71.812β = 95.55
c = 78.379γ = 118.9
Software Package:
Software NamePurpose
BUSTERrefinement
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release