6WIO

Fab antigen complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing.

Lieu, R.Antonysamy, S.Druzina, Z.Ho, C.Kang, N.R.Pustilnik, A.Wang, J.Atwell, S.

(2020) PLoS One 15: e0232311-e0232311

  • DOI: https://doi.org/10.1371/journal.pone.0232311
  • Primary Citation of Related Structures:  
    6WG8, 6WGB, 6WGJ, 6WGK, 6WGL, 6WIO, 6WIR

  • PubMed Abstract: 

    Antibody therapeutics are one of the most important classes of drugs. Antibody structures have become an integral part of predicting the behavior of potential therapeutics, either directly or as the basis of modeling. Structures of Fab:antigen complexes have even greater value. While the crystallization and structure determination of Fabs is easy relative to many other protein classes, especially membrane proteins, broad screening and optimization of crystalline hits is still necessary. Through a comprehensive review of rabbit Fab crystal contacts and their incompatibility with human Fabs, we identified a small secondary structural element from the rabbit light chain constant domain potentially responsible for hindering the crystallization of human Fabs. Upon replacing the human kappa constant domain FG loop (HQGLSSP) with the two residue shorter rabbit loop (QGTTS), we dramatically improved the crystallization of human Fabs and Fab:antigen complexes. Our design, which we call "Crystal Kappa", enables rapid crystallization of human fabs and fab complexes in a broad range of conditions, with less material in smaller screens or from dilute solutions.


  • Organizational Affiliation

    Biotechnology Discovery Research, Applied Molecular Evolution, Eli Lilly and Company, San Diego, CA, United States of America.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Heavy chain230Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Light chain213Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-17A161Homo sapiensMutation(s): 0 
Gene Names: IL17ACTLA8IL17
UniProt & NIH Common Fund Data Resources
Find proteins for Q16552 (Homo sapiens)
Explore Q16552 
Go to UniProtKB:  Q16552
PHAROS:  Q16552
GTEx:  ENSG00000112115 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16552
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.256α = 90
b = 73.256β = 90
c = 316.384γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description