5N7W

Computationally designed functional antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Computational Design of Epitope-Specific Functional Antibodies.

Nimrod, G.Fischman, S.Austin, M.Herman, A.Keyes, F.Leiderman, O.Hargreaves, D.Strajbl, M.Breed, J.Klompus, S.Minton, K.Spooner, J.Buchanan, A.Vaughan, T.J.Ofran, Y.

(2018) Cell Rep 25: 2121-2131.e5

  • DOI: 10.1016/j.celrep.2018.10.081

  • PubMed Abstract: 
  • The ultimate goal of protein design is to introduce new biological activity. We propose a computational approach for designing functional antibodies by focusing on functional epitopes, integrating large-scale statistical analysis with multiple struct ...

    The ultimate goal of protein design is to introduce new biological activity. We propose a computational approach for designing functional antibodies by focusing on functional epitopes, integrating large-scale statistical analysis with multiple structural models. Machine learning is used to analyze these models and predict specific residue-residue contacts. We use this approach to design a functional antibody to counter the proinflammatory effect of the cytokine interleukin-17A (IL-17A). X-ray crystallography confirms that the designed antibody binds the targeted epitope and the interaction is mediated by the designed contacts. Cell-based assays confirm that the antibody is functional. Importantly, this approach does not rely on a high-quality 3D model of the designed complex or even a solved structure of the target. As demonstrated here, this approach can be used to design biologically active antibodies, removing some of the main hurdles in antibody design and in drug discovery.


    Organizational Affiliation

    Graduate School of Science and Molecular Chirality Research Center, Chiba University, Inage, Chiba, Japan.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Institute of Advanced Energy and Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,Biolojic Design, Ltd., 12 Hamada Street, Rehovot 7670314, Israel.,Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India and snjam@barc.gov.in.,Japan Science and Technology Agency (JST) and Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea. yok5@snu.ac.kr.,Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 17, 38106, Braunschweig, Germany.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,From the High Pressure and Synchrotron Radiation Physics Division and ravimakde@rrcat.gov.in.,RIKEN, SPring-8 Center, Hyogo, Japan.,Department of Chemistry, University of California, San Diego, La Jolla, California, 92093.,Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.,Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California, 92093.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.,From the High Pressure and Synchrotron Radiation Physics Division and.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. r.suno@mfour.med.kyoto-u.ac.jp.,School of Biochemistry, Devi Ahilya University, Indore 452001, India.,Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 17, 38106, Braunschweig, Germany. U.Rau@tu-bs.de.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, 92093.,Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA.,Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, Japan.,Protech Inc., Yongeon 103 Daehangno, Jongno-gu, Seoul, 110-799, Republic of Korea. yok5@snu.ac.kr.,Cancer Metabolism and Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.,AstraZeneca R&D, Darwin Building Cambridge Science Park, Milton Road, Cambridge CB4 0WG, UK.,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA. tatiana.kutateladze@ucdenver.edu.,Biolojic Design, Ltd., 12 Hamada Street, Rehovot 7670314, Israel; The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan 52900, Israel. Electronic address: yanay@ofranlab.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antibody Fragment Heavy Chain
A, H
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody Fragment Light Chain
B, L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Interleukin-17A
X, Y
155Homo sapiensMutation(s): 0 
Gene Names: IL17A (CTLA8, IL17)
Find proteins for Q16552 (Homo sapiens)
Go to Gene View: IL17A
Go to UniProtKB:  Q16552
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.240α = 90.00
b = 199.980β = 96.42
c = 76.350γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references
  • Version 1.2: 2018-12-05
    Type: Data collection, Database references