PDBsum entry 6mxr

Immune system

PDB id: 6mxr

Contents

Protein chains

219 a.a.

218 a.a.

Ligands

EDO

Metals

_NA

_CL ×2

Waters ×722

PDB id:

6mxr

Name:

Immune system

Title:

Crystal structure of the dimeric bh1-fab variant [hc-y33w,hc-d98m,hc- g99m]

Structure:

Anti-vegf-a fab fragment bh1 heavy chain. Chain: h, a. Engineered: yes. Mutation: yes. Anti-vegf-a fab fragment bh1 light chain. Chain: l, b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: cho-3e7. Expression_system_cell_line: cho-3e7

Resolution:

2.04Å R-factor: 0.169 R-free: 0.200

Authors:

R.Shi

Key ref:

J.D.Schrag et al. (2019). Binding symmetry and surface flexibility mediate antibody self-association. MAbs, 11, 1300-1318. PubMed id: 31318308 DOI: 10.1080/19420862.2019.1632114

Date:

31-Oct-18 Release date: 31-Jul-19

Protein chains

V9HW68  (V9HW68_HUMAN) -  Epididymis luminal protein 214 from Homo sapiens

Seq: 470 a.a.

Struc: 219 a.a.*

Protein chains

Q7Z3Y4  (Q7Z3Y4_HUMAN) -  Ig-like domain-containing protein from Homo sapiens

Seq: 236 a.a.

Struc: 218 a.a.*

* PDB and UniProt seqs differ at 55 residue positions (black crosses)

DOI no: 10.1080/19420862.2019.1632114

MAbs 11:1300-1318 (2019)

PubMed id: 31318308

Binding symmetry and surface flexibility mediate antibody self-association.

J.D.Schrag, M.Ã.ˆ.Picard, F.Gaudreault, L.P.Gagnon, J.Baardsnes, M.S.Manenda, J.Sheff, C.Deprez, C.Baptista, H.Hogues, J.F.Kelly, E.O.Purisima, R.Shi, T.Sulea.

ABSTRACT

Solution stability is an important factor in the optimization of engineered biotherapeutic candidates such as monoclonal antibodies because of its possible effects on manufacturability, pharmacology, efficacy and safety. A detailed atomic understanding of the mechanisms governing self-association of natively folded protein monomers is required to devise predictive tools to guide screening and re-engineering along the drug development pipeline. We investigated pairs of affinity-matured full-size antibodies and observed drastically different propensities to aggregate from variants differing by a single amino-acid. Biophysical testing showed that antigen-binding fragments (Fabs) from the aggregating antibodies also reversibly associated with equilibrium dissociation constants in the low-micromolar range. Crystal structures (PDB accession codes 6MXR, 6MXS, 6MY4, 6MY5) and bottom-up hydrogen-exchange mass spectrometry revealed that Fab self-association occurs in a symmetric mode that involves the antigen complementarity-determining regions. Subtle local conformational changes incurred upon point mutation of monomeric variants foster formation of complementary polar interactions and hydrophobic contacts to generate a dimeric Fab interface. Testing of popular in silico tools generally indicated low reliabilities for predicting the aggregation propensities observed. A structure-aggregation data set is provided here in order to stimulate further improvements of in silico tools for prediction of native aggregation. Incorporation of intermolecular docking, conformational flexibility, and short-range packing interactions may all be necessary features of the ideal algorithm.