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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1073/pnas.1901734117
  • Structures With Same Primary Citation

  • 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 hu ...

    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.


    Related Citations: 
    • Monoclonal antibody to an endogenous bufadienolide, marinobufagenin, reverses preeclampsia-induced Na/K-ATPase inhibition and lowers blood pressure in NaCl-sensitive hypertension.
      Fedorova, O.V., Simbirtsev, A.S., Kolodkin, N.I., Kotov, A.Y., Agalakova, N.I., Kashkin, V.A., Tapilskaya, N.I., Bzhelyansky, A., Reznik, V.A., Frolova, E.V., Nikitina, E.R., Budny, G.V., Longo, D.L., Lakatta, E.G., Bagrov, A.Y.
      (2008) J Hypertens 26: 2414

    Organizational Affiliation

    Regeneron Tech Centers, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IgG4 C regionA, H222Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
3E9 antibody Fab light chainB, L219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P4S
Query on P4S

Download CCD File 
B, H
(3beta,5beta,14alpha,15beta)-3,5-dihydroxy-14,15-epoxybufa-20,22-dienolide
C24 H32 O5
JMNQTHQLNRILMH-OBBGIPBRSA-N
 Ligand Interaction
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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Entry History 

Deposition Data

Revision History 

  • 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