6P79 | pdb_00006p79

Engineered single chain antibody C9+C14 ScFv

• PDB DOI: https://doi.org/10.2210/pdb6P79/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-06-05 Released: 2020-04-15 
• Deposition Author(s): Zhang, Y., Li, W., Marshall, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Computer-based Engineering of Thermostabilized Antibody Fragments.

Lee, J., Der, B.S., Karamitros, C.S., Li, W., Marshall, N.M., Lungu, O.I., Miklos, A.E., Xu, J., Kang, T.H., Lee, C.H., Tan, B., Hughes, R.A., Jung, S.T., Ippolito, G.C., Gray, J.J., Zhang, Y., Kuhlman, B., Georgiou, G., Ellington, A.D.

(2020) AIChE J 66

• PubMed: 32336757 
• DOI: https://doi.org/10.1002/aic.16864
• Primary Citation Related Structures: 
  6P79


• PubMed Abstract: 
  

  We used the molecular modeling program Rosetta to identify clusters of amino acid substitutions in antibody fragments (scFvs and scAbs) that improve global protein stability and resistance to thermal deactivation. Using this methodology, we increased the melting temperature (T _m ) and resistance to heat treatment of an antibody fragment that binds to the Clostridium botulinum hemagglutinin protein (anti-HA33). Two designed antibody fragment variants with two amino acid replacement clusters, designed to stabilize local regions, were shown to have both higher T _m compared to the parental scFv and importantly, to retain full antigen binding activity after 2 hours of incubation at 70 °C. The crystal structure of one thermostabilized scFv variants was solved at 1.6 Å and shown to be in close agreement with the RosettaAntibody model prediction.

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Organizational Affiliation: 
• Thayer School of Engineering, Dartmouth College, Hanover, NH 03755.
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599.
Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712.
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.
U.S. Army Combat Capabilities Development Command Chemical Biological Center, APGEA, MD 21010.
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MA 21218.
Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seongbuk-gu, Seoul 02707, Republic of Korea.
US Army Research Laboratory, Austin, TX 78712.
Applied Research Laboratories, The University of Texas at Austin, Austin, TX 78712.
Department of Biomedical Science, Graduate School of Medicine, Korea University, Seoul 02841, Republic of Korea.
Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712.
Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712.
Department of Chemistry, The University of Texas at Austin, Austin, TX 78712.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.8 kDa 
• Atom Count: 1,938 
• Modeled Residue Count: 227 
• Deposited Residue Count: 247 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered antibody heavy chain	A [auth H]	120	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered antibody light chain	B [auth L]	127	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.282	α = 90
b = 66.696	β = 90
c = 74.955	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Zhang, Y., Li, W., Marshall, N.

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary