4ZFO | pdb_00004zfo

J22.9-xi: chimeric mouse/human antibody against human BCMA (CD269)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.209 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4ZFO

This is version 1.3 of the entry. See complete history

Literature

Potent anti-tumor response by targeting B cell maturation antigen (BCMA) in a mouse model of multiple myeloma.

Oden, F.Marino, S.F.Brand, J.Scheu, S.Kriegel, C.Olal, D.Takvorian, A.Westermann, J.Yilmaz, B.Hinz, M.Daumke, O.Hopken, U.E.Muller, G.Lipp, M.

(2015) Mol Oncol 9: 1348-1358

  • DOI: https://doi.org/10.1016/j.molonc.2015.03.010
  • Primary Citation Related Structures: 
    4ZFO

  • PubMed Abstract: 

    Multiple myeloma (MM) is an aggressive incurable plasma cell malignancy with a median life expectancy of less than seven years. Antibody-based therapies have demonstrated substantial clinical benefit for patients with hematological malignancies, particular in B cell Non-Hodgkin's lymphoma. The lack of immunotherapies specifically targeting MM cells led us to develop a human-mouse chimeric antibody directed against the B cell maturation antigen (BCMA), which is almost exclusively expressed on plasma cells and multiple myeloma cells. The high affinity antibody blocks the binding of the native ligands APRIL and BAFF to BCMA. This finding is rationalized by the high resolution crystal structure of the Fab fragment in complex with the extracellular domain of BCMA. Most importantly, the antibody effectively depletes MM cells in vitro and in vivo and substantially prolongs tumor-free survival under therapeutic conditions in a xenograft mouse model. A BCMA-antibody-based therapy is therefore a promising option for the effective treatment of multiple myeloma and autoimmune diseases.


  • Organizational Affiliation
    • Max-Delbrück-Center of Molecular Medicine (MDC), Department of Tumor Genetics and Immunogenetics, Robert-Rössle-Strasse 10, 13125 Berlin, Germany. Electronic address: felix.oden@mdc-berlin.de.

Macromolecule Content 

  • Total Structure Weight: 106.71 kDa 
  • Atom Count: 7,946 
  • Modeled Residue Count: 929 
  • Deposited Residue Count: 977 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 17A [auth F],
F [auth K]
54Homo sapiensMutation(s): 0 
Gene Names: TNFRSF17BCMBCMA
UniProt & NIH Common Fund Data Resources
Find proteins for Q02223 (Homo sapiens)
Explore Q02223 
Go to UniProtKB:  Q02223
PHAROS:  Q02223
GTEx:  ENSG00000048462 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02223
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
J22.9-xi Fab, Light ChainB [auth L]214Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
J22.9-xi Fab, Heavy ChainC [auth H],
E [auth A]
221Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
J22.9-xi Fab, Light ChainD [auth B]213Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.209 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.801α = 90
b = 110.139β = 90
c = 137.279γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
HFSPOGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary