8VEG

Crystal structure of an engineered conformationally rigid anti-Tryptase Fab variant E104.v1.4DS.S112F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Disulfi de constrained Fabs overcome target size limitation for high-resolution single-particle cryo-EM.

Kung, J.E.Johnson, M.C.Jao, C.C.Arthur, C.P.Tegunov, D.Rohou, A.Sudhamsu, J.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.05.10.593593
  • Primary Citation of Related Structures:  
    8VEG, 8VGE, 8VGF, 8VGG, 8VGH, 8VGI, 8VGJ, 8VGK, 8VGL, 8VGM, 8VGN, 8VGO, 8VGP, 8VGQ

  • PubMed Abstract: 

    High-resolution structures of proteins are critical to understanding molecular mechanisms of biological processes and in the discovery of therapeutic molecules. Cryo-EM has revolutionized structure determination of large proteins and their complexes 1 , but a vast majority of proteins that underlie human diseases are small (< 50 kDa) and usually beyond its reach due to low signal-to-noise images and difficulties in particle alignment 2 . Current strategies to overcome this problem increase the overall size of small protein targets using scaffold proteins that bind to the target, but are limited by inherent flexibility and not being bound to their targets in a rigid manner, resulting in the target being poorly resolved compared to the scaffolds 3-11 . Here we present an iteratively engineered molecular design for transforming Fabs (antibody fragments), into conformationally rigid scaffolds (Rigid-Fabs) that, when bound to small proteins (~20 kDa), can enable high-resolution structure determination using cryo-EM. This design introduces multiple disulfide bonds at strategic locations, generates a well-folded Fab constrained into a rigid conformation and can be applied to Fabs from various species, isotypes and chimeric Fabs. We present examples of the Rigid Fab design enabling high-resolution (2.3-2.5 Å) structures of small proteins, Ang2 (26 kDa) and KRAS (21 kDa) by cryo-EM. The strategies for designing disulfide constrained Rigid Fabs in our work thus establish a general approach to overcome the target size limitation of single particle cryo-EM.


  • Organizational Affiliation

    Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab E104.v1.4DS.S112F light chain217Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab E104.v1.4DS.S112F heavy chain238Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.342α = 90
b = 116.342β = 90
c = 136.046γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Database references