4QCI

PDGF-B blocking antibody bound to PDGF-BB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Characterization of Binding Mode of Action of a Blocking Anti-Platelet-Derived Growth Factor (PDGF)-B Monoclonal Antibody, MOR8457, Reveals Conformational Flexibility and Avidity Needed for PDGF-BB To Bind PDGF Receptor-beta.

Kuai, J.Mosyak, L.Brooks, J.Cain, M.Carven, G.J.Ogawa, S.Ishino, T.Tam, M.Lavallie, E.R.Yang, Z.Ponsel, D.Rauchenberger, R.Arch, R.Pullen, N.

(2015) Biochemistry 54: 1918-1929

  • DOI: https://doi.org/10.1021/bi5015425
  • Primary Citation of Related Structures:  
    4QCI

  • PubMed Abstract: 

    Platelet derived growth factor-BB (PDGF-BB) is an important mitogen and cell survival factor during development. PDGF-BB binds PDGF receptor-β (PDGFRβ) to trigger receptor dimerization and tyrosine kinase activation. We present the pharmacological and biophysical characterization of a blocking PDGF-BB monoclonal antibody, MOR8457, and contrast this to PDGFRβ. MOR8457 binds to PDGF-BB with high affinity and selectivity, and prevents PDGF-BB induced cell proliferation competitively and with high potency. The structural characterization of the MOR8457-PDGF-BB complex indicates that MOR8457 binds with a 2:1 stoichiometry, but that binding of a single MOR8457 moiety is sufficient to prevent binding to PDGFRβ. Comparison of the MOR8457-PDGF-BB structure with that of the PDGFRβ-PDGF-BB complex suggested the potential reason for this was a substantial bending and twisting of PDGF-BB in the MOR8457 structure, relative to the structures of PDGF-BB alone, bound to a PDGF-BB aptamer or PDGFRβ, which makes it nonpermissive for PDGFRβ binding. These biochemical and structural data offer insights into the permissive structure of PDGF-BB needed for agonism as well as strategies for developing specific PDGF ligand antagonists.


  • Organizational Affiliation

    ‡Scholar Rock LLC, 300 Technology Square, Cambridge, Massachusetts 02142, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-PDGF-BB antibody - Light ChainA,
F [auth L]
209Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
anti-PDGF-BB antibody - Heavy chainB,
E [auth H]
223Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet-derived growth factor subunit B
C, D
110Homo sapiensMutation(s): 0 
Gene Names: PDGFBPDGF2SIS
UniProt & NIH Common Fund Data Resources
Find proteins for P01127 (Homo sapiens)
Explore P01127 
Go to UniProtKB:  P01127
PHAROS:  P01127
GTEx:  ENSG00000100311 
Entity Groups  
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UniProt GroupP01127
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.15α = 90
b = 68.47β = 97.56
c = 95.25γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
BUSTERrefinement
autoPROCdata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2018-02-14
    Changes: Experimental preparation
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Refinement description