PDBsum entry 5o4e

Immune system

PDB id: 5o4e

Contents

Protein chains

209 a.a.

216 a.a.

181 a.a.

95 a.a.

Ligands

NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC ×2

MAN-NAG

NAG-NAG-BMA-MAN-NAG-MAN

MPD ×10

MRD

CAC ×2

TRS

Waters ×242

PDB id:

5o4e

Name:

Immune system

Title:

Crystal structure of vegf in complex with heterodimeric fcab janusct6

Structure:

Immunoglobulin gamma-1 heavy chain. Chain: a. Synonym: immunoglobulin gamma-1 heavy chain nie. Engineered: yes. Mutation: yes. Immunoglobulin gamma-1 heavy chain. Chain: b, d. Synonym: immunoglobulin gamma-1 heavy chain nie. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293-6e. Expression_system_organ: kidney. Gene: vegfa, vegf. Expressed in: escherichia coli.

Resolution:

2.15Å R-factor: 0.201 R-free: 0.236

Authors:

G.Mlynek,E.Lobner,K.Kubinger,A.Humm,C.Obinger,K.Djinovic-Carugo

Key ref:

E.Lobner et al. (2017). Two-faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 Å crystal structure of the complex. MAbs, 9, 1088-1104. PubMed id: 28816592

Date:

29-May-17 Release date: 30-Aug-17

Protein chain

P0DOX5  (IGG1_HUMAN) -  Immunoglobulin gamma-1 heavy chain from Homo sapiens

Seq: 449 a.a.

Struc: 209 a.a.*

Protein chains

P0DOX5  (IGG1_HUMAN) -  Immunoglobulin gamma-1 heavy chain from Homo sapiens

Seq: 449 a.a.

Struc: 216 a.a.*

Protein chain

P0DOX5  (IGG1_HUMAN) -  Immunoglobulin gamma-1 heavy chain from Homo sapiens

Seq: 449 a.a.

Struc: 181 a.a.*

Protein chains

P15692  (VEGFA_HUMAN) -  Vascular endothelial growth factor A, long form from Homo sapiens

Seq: 395 a.a.

Struc: 95 a.a.*

* PDB and UniProt seqs differ at 37 residue positions (black crosses)

MAbs 9:1088-1104 (2017)

PubMed id: 28816592

Two-faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 Å crystal structure of the complex.

E.Lobner, A.S.Humm, G.Mlynek, K.Kubinger, M.Kitzmüller, M.W.Traxlmayr, K.Djinović-Carugo, C.Obinger.

ABSTRACT

Fcabs (Fc domain with antigen-binding sites) are promising novel therapeutics. By engineering of the C-terminal loops of the CH3 domains, 2 antigen binding sites can be inserted in close proximity. To elucidate the binding mode(s) between homodimeric Fcabs and small homodimeric antigens, the interaction between the Fcabs 448 and CT6 (having the AB, CD and EF loops and the C-termini engineered) with homodimeric VEGF was investigated. The crystal structures of these Fcabs, which form polymers with the antigen VEGF in solution, were determined. However, construction of heterodimeric Fcabs (JanusFcabs: one chain Fc-wt, one chain VEGF-binding) results in formation of distinct JanusFcab-VEGF complexes (2:1), which allowed elucidation of the crystal structure of the JanusCT6-VEGF complex at 2.15 Å resolution. VEGF binding to Janus448 and JanusCT6 is shown to be entropically unfavorable, but enthalpically favorable. Structure-function relationships are discussed with respect to Fcab design and engineering strategies.