6PYD

Structure of 3E9 antibody Fab bound to marinobufagenin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Kappa-on-Heavy (KoH) bodies are a distinct class of fully-human antibody-like therapeutic agents with antigen-binding properties.

Macdonald, L.E.Meagher, K.A.Franklin, M.C.Levenkova, N.Hansen, J.Badithe, A.T.Zhong, M.Krueger, P.Rafique, A.Tu, N.Shevchuk, J.Wadhwa, S.Ehrlich, G.Bautista, J.Grant, C.Esau, L.Poueymirou, W.T.Auerbach, W.Morton, L.Babb, R.Chen, G.Huang, T.MacDonald, D.Graham, K.Gurer, C.Voronina, V.A.McWhirter, J.R.Guo, C.Yancopoulos, G.D.Murphy, A.J.

(2020) Proc Natl Acad Sci U S A 117: 292-299

  • DOI: https://doi.org/10.1073/pnas.1901734117
  • Primary Citation of Related Structures:  
    6PYC, 6PYD

  • PubMed Abstract: 

    We describe a Kappa-on-Heavy (KoH) mouse that produces a class of highly diverse, fully human, antibody-like agents. This mouse was made by replacing the germline variable sequences of both the Ig heavy-chain (IgH) and Ig kappa (IgK) loci with the human IgK germline variable sequences, producing antibody-like molecules with an antigen binding site made up of 2 kappa variable domains. These molecules, named KoH bodies, structurally mimic naturally existing Bence-Jones light-chain dimers in their variable domains and remain wild-type in their antibody constant domains. Unlike artificially diversified, nonimmunoglobulin alternative scaffolds (e.g., DARPins), KoH bodies consist of a configuration of normal Ig scaffolds that undergo natural diversification in B cells. Monoclonal KoH bodies have properties similar to those of conventional antibodies but exhibit an enhanced ability to bind small molecules such as the endogenous cardiotonic steroid marinobufagenin (MBG) and nicotine. A comparison of crystal structures of MBG bound to a KoH Fab versus a conventional Fab showed that the KoH body has a much deeper binding pocket, allowing MBG to be held 4 Å further down into the combining site between the 2 variable domains.


  • Organizational Affiliation

    Regeneron Tech Centers, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591 lynn.macdonald@regeneron.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IgG4 C regionA [auth H],
C [auth A]
222Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3E9 antibody Fab light chainB [auth L],
D [auth B]
219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P4S (Subject of Investigation/LOI)
Query on P4S

Download Ideal Coordinates CCD File 
E [auth H],
F [auth B]
(3beta,5beta,14alpha,15beta)-3,5-dihydroxy-14,15-epoxybufa-20,22-dienolide
C24 H32 O5
JMNQTHQLNRILMH-OBBGIPBRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.92α = 97.37
b = 67.69β = 106.35
c = 71.986γ = 107
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Database references
  • Version 1.2: 2020-01-22
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description