PDBsum entry 5djc

Immune system

PDB id: 5djc

Contents

Protein chains

207 a.a.

206 a.a.

13 a.a.

Ligands

NAG-NAG-BMA-MAN-NAG-GAL-MAN-FUC ×4

Metals

IOD

Waters ×189

PDB id:

5djc

Name:

Immune system

Title:

Fc heterodimer design 8.1 l368v/y407a + t366v/k409f

Structure:

Ig gamma-1 chain c region. Chain: a, d. Fragment: unp residues 104-330. Engineered: yes. Mutation: yes. Ig gamma-1 chain c region. Chain: b, e. Fragment: unp residues 104-330. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ighg1. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293. Synthetic: yes. Synthetic construct.

Resolution:

2.10Å R-factor: 0.232 R-free: 0.285

Authors:

S.Atwell,A.Leaver-Fay,K.J.Froning,H.Aldaz,A.Pustilnik,F.Lu,F.Huang, R.Yuan,S.H.Dhanani,A.K.Chamberlain,J.R.Fitchett,B.Gutierrez, J.Hendle,E.Secrist,S.J.Demarest,B.Kuhlman

Key ref:

A.Leaver-Fay et al. (2016). Computationally Designed Bispecific Antibodies using Negative State Repertoires. Structure, 24, 641-651. PubMed id: 26996964 DOI: 10.1016/j.str.2016.02.013

Date:

01-Sep-15 Release date: 30-Mar-16

Protein chains

P01857  (IGHG1_HUMAN) -  Immunoglobulin heavy constant gamma 1 from Homo sapiens

Seq: 399 a.a.

Struc: 207 a.a.*

Protein chains

P01857  (IGHG1_HUMAN) -  Immunoglobulin heavy constant gamma 1 from Homo sapiens

Seq: 399 a.a.

Struc: 206 a.a.*

Protein chains

No UniProt id for this chain

Struc: 13 a.a.

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

DOI no: 10.1016/j.str.2016.02.013

Structure 24:641-651 (2016)

PubMed id: 26996964

Computationally Designed Bispecific Antibodies using Negative State Repertoires.

A.Leaver-Fay, K.J.Froning, S.Atwell, H.Aldaz, A.Pustilnik, F.Lu, F.Huang, R.Yuan, S.Hassanali, A.K.Chamberlain, J.R.Fitchett, S.J.Demarest, B.Kuhlman.

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.