6AZ2 | pdb_00006az2

Crystal structure of Asf1-Fab 12E complex

• PDB DOI: https://doi.org/10.2210/pdb6AZ2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-09 Released: 2018-01-10 
• Deposition Author(s): Bailey, L.J., Kossiakoff, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

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 Biology 430: 337-347

• PubMed: 29273204 
• DOI: https://doi.org/10.1016/j.jmb.2017.12.012
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
Ben May Institute for Cancer Research, University of Chicago, Chicago, IL 60637, USA.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA; University of Gdansk and Medical University of Gdansk, International Faculty of Biotechnology, Gdansk, Poland.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA; Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Krakow, Poland.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 130.59 kDa 
• Atom Count: 8,950 
• Modeled Residue Count: 1,131 
• Deposited Residue Count: 1,196 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Heavy Chain	A, B [auth C]	229	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone chaperone ASF1	C [auth B], D	154	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: ASF1, CIA1, YJL115W, J0755
UniProt
Find proteins for P32447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32447  Go to UniProtKB:  P32447

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Light Chain	E, F	215	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.666	α = 90
b = 109.743	β = 90
c = 122.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-10 
Deposition Author(s): Bailey, L.J., Kossiakoff, A.A.

Revision History  

• 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