5DK0

Fc Heterodimer Design 20.8.34 Y349S/T366M/K370Y/K409V + E356G/E357D/S364Q/Y407A

Summary for 5DK0

• Entry DOI: 10.2210/pdb5dk0/pdb
• Related: 5DI8 5DJ0 5DJ2 5DJ6 5DJ8 5DJA 5DJC 5DJD 5DJX 5DJY 5DJZ 5DK2 5DVK 5DVL 5DVM 5DVN 5DVO
• Descriptor: Ig gamma-1 chain C region, Fc-III peptide, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: heterodimer, immunoglobulin, ch3, fc, bispecific antibody, immune system
• Biological source: Homo sapiens (Human); More
• Cellular location: Secreted: P01857 P01857
• Total number of polymer chains: 3
• Total formula weight: 56794.47

Authors

Atwell, S.,Leaver-Fay, A.,Froning, K.J.,Aldaz, H.,Pustilnik, A.,Lu, F.,Huang, F.,Yuan, R.,Dhanani, S.H.,Chamberlain, A.K.,Fitchett, J.R.,Gutierrez, B.,Hendle, J.,Demarest, S.J.,Kuhlman, B. (deposition date: 2015-09-02, release date: 2016-03-30, Last modification date: 2024-11-06)

Primary citation

Leaver-Fay, A.,Froning, K.J.,Atwell, S.,Aldaz, H.,Pustilnik, A.,Lu, F.,Huang, F.,Yuan, R.,Hassanali, S.,Chamberlain, A.K.,Fitchett, J.R.,Demarest, S.J.,Kuhlman, B.
Computationally Designed Bispecific Antibodies using Negative State Repertoires.
Structure, 24:641-651, 2016

PubMed Abstract: A challenge in the structure-based design of specificity is modeling the negative states, i.e., the complexes that you do not want to form. This is a difficult problem because mutations predicted to destabilize the negative state might be accommodated by small conformational rearrangements. To overcome this challenge, we employ an iterative strategy that cycles between sequence design and protein docking in order to build up an ensemble of alternative negative state conformations for use in specificity prediction. We have applied our technique to the design of heterodimeric CH3 interfaces in the Fc region of antibodies. Combining computationally and rationally designed mutations produced unique designs with heterodimer purities greater than 90%. Asymmetric Fc crystallization was able to resolve the interface mutations; the heterodimer structures confirmed that the interfaces formed as designed. With these CH3 mutations, and those made at the heavy-/light-chain interface, we demonstrate one-step synthesis of four fully IgG-bispecific antibodies.

PubMed: 26996964
DOI: 10.1016/j.str.2016.02.013

Experimental method

X-RAY DIFFRACTION (2.3 Å)