6AZ2

Crystal structure of Asf1-Fab 12E complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.

Bailey, L.J.Sheehy, K.M.Dominik, P.K.Liang, W.G.Rui, H.Clark, M.Jaskolowski, M.Kim, Y.Deneka, D.Tang, W.J.Kossiakoff, A.A.

(2018) J Mol Biol 430: 337-347

  • DOI: https://doi.org/10.1016/j.jmb.2017.12.012
  • Primary Citation of Related Structures:  
    5CJO, 6AYZ, 6AZ2

  • PubMed Abstract: 

    Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the "elbow" regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab-antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Heavy ChainA,
B [auth C]
229Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone chaperone ASF1C [auth B],
D
154Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASF1CIA1YJL115WJ0755
UniProt
Find proteins for P32447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32447 
Go to UniProtKB:  P32447
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32447
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Light Chain
E, F
215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.666α = 90
b = 109.743β = 90
c = 122.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary