5CBA

3B4 in complex with CXCL13 - 3B4-CXCL13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv).

Tu, C.Terraube, V.Tam, A.S.Stochaj, W.Fennell, B.J.Lin, L.Stahl, M.LaVallie, E.R.Somers, W.Finlay, W.J.Mosyak, L.Bard, J.Cunningham, O.

(2016) J Biol Chem 291: 1267-1276

  • DOI: https://doi.org/10.1074/jbc.M115.688010
  • Primary Citation of Related Structures:  
    5CBA, 5CBE

  • PubMed Abstract: 

    Fully-human single-chain Fv (scFv) proteins are key potential building blocks of bispecific therapeutic antibodies, but they often suffer from manufacturability and clinical development limitations such as instability and aggregation. The causes of these scFv instability problems, in proteins that should be theoretically stable, remains poorly understood. To inform the future development of such molecules, we carried out a comprehensive structural analysis of the highly stabilized anti-CXCL13 scFv E10. E10 was derived from the parental 3B4 using complementarity-determining region (CDR)-restricted mutagenesis and tailored selection and screening strategies, and carries four mutations in VL-CDR3. High-resolution crystal structures of parental 3B4 and optimized E10 scFvs were solved in the presence and absence of human CXCL13. In parallel, a series of scFv mutants was generated to interrogate the individual contribution of each of the four mutations to stability and affinity improvements. In combination, these analyses demonstrated that the optimization of E10 was primarily mediated by removing clashes between both the VL and the VH, and between the VL and CXCL13. Importantly, a single, germline-encoded VL-CDR3 residue mediated the key difference between the stable and unstable forms of the scFv. This work demonstrates that, aside from being the critical mediators of specificity and affinity, CDRs may also be the primary drivers of biotherapeutic developability.


  • Organizational Affiliation

    From Global Biotherapeutics Technologies, Pfizer R&D, Cambridge, Massachusetts 02140 and.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3b4 heavy chain
A, C
142Homo sapiensMutation(s): 0 
Gene Names: IGHV1-69-2
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J2H0 (Homo sapiens)
Explore A0A0B4J2H0 
Go to UniProtKB:  A0A0B4J2H0
GTEx:  ENSG00000280411 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B4J2H0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3b4 light chain
B, D
117Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01704 (Homo sapiens)
Explore P01704 
Go to UniProtKB:  P01704
GTEx:  ENSG00000211666 
Entity Groups  
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UniProt GroupP01704
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
C-X-C motif chemokine 13
E, F
88Homo sapiensMutation(s): 0 
Gene Names: CXCL13BCA1BLCSCYB13
UniProt & NIH Common Fund Data Resources
Find proteins for O43927 (Homo sapiens)
Explore O43927 
Go to UniProtKB:  O43927
PHAROS:  O43927
GTEx:  ENSG00000156234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43927
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.35α = 90
b = 55.68β = 120.56
c = 112.77γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.2: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary