Biomaterial Database

Crystal structures of a llama VHH antibody BCD090-M2 targeting human ErbB3 receptor. 2018

Igor E Eliseev, and Anna N Yudenko, and Vera V Vysochinskaya, and Anna A Svirina, and Anna V Evstratyeva, and Maria S Drozhzhachih, and Elena A Krendeleva, and Anna K Vladimirova, and Timofey A Nemankin, and Viktoria M Ekimova, and Andrey B Ulitin, and Maria I Lomovskaya, and Pavel A Yakovlev, and Anton S Bukatin, and Nickolay A Knyazev, and Fedor V Moiseenko, and Oleg B Chakchir

St. Petersburg National Research Academic University RAS, St. Petersburg, 194021, Russian Federation.

Background: The ability of ErbB3 receptor to functionally complement ErbB1-2 and induce tumor resistance to their inhibitors makes it a unique target in cancer therapy by monoclonal antibodies. Here we report the expression, purification and structural analysis of a new anti-ErbB3 single-chain antibody. Methods: The VHH fragment of the antibody was expressed in E. coli SHuffle cells as a SUMO fusion, cleaved by TEV protease and purified to homogeneity. Binding to the extracellular domain of ErbB3 was studied by surface plasmon resonance. For structural studies, the antibody was crystallized by hanging-drop vapor diffusion in two different forms. Results: We developed a robust and efficient system for recombinant expression of single-domain antibodies. The purified antibody was functional and bound ErbB3 with K =15±1 nM. The crystal structures of the VHH antibody in space groups C2 and P1 were solved by molecular replacement at 1.6 and 1.9 Å resolution. The high-quality electron density maps allowed us to build precise atomic models of the antibody and the putative paratope. Surprisingly, the CDR H2 existed in multiple distant conformations in different crystal forms, while the more complex CDR H3 had a low structural variability. The structures were deposited under PDB entry codes 6EZW and 6F0D. Conclusions: Our results may facilitate further mechanistic studies of ErbB3 inhibition by single-chain antibodies. Besides, the solved structures will contribute to datasets required to develop new computational methods for antibody modeling and design.

UI	MeSH Term	Description	Entries
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D011487	Protein Conformation	The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).	Conformation, Protein,Conformations, Protein,Protein Conformations
D002161	Camelids, New World	Camelidae of the Americas. The extant species are those originating from South America and include alpacas, llamas, guanicos, and vicunas.	Alpacas,Guanacos,Llamas,Lama glama,Lama glama guanicoe,Lama guanicoe,Lama pacos,Vicugna pacos,Vicugna vicugna,Vicunas,Alpaca,Camelid, New World,Guanaco,Llama,New World Camelid,New World Camelids,Vicuna
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000595	Amino Acid Sequence	The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.	Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D000911	Antibodies, Monoclonal	Antibodies produced by a single clone of cells.	Monoclonal Antibodies,Monoclonal Antibody,Antibody, Monoclonal
D061905	Single-Domain Antibodies	An immunoglobulin fragment composed of one variable domain from an IMMUNOGLOBULIN HEAVY CHAIN or IMMUNOGLOBULIN LIGHT CHAIN.	Single-Domain Antibody,VHH Antibodies,VHH Antibody,Immunoglobulin VH Domain Fragments,Immunoglobulin VL Domain Fragments,Nanobodies,VH Domain Fragments,VHH Fragments,VHH Immunoglobulin Fragments,VL Domain Fragments,VNAR Fragments,VNAR Immunoglobulin Fragments,Antibody, Single-Domain,Antibody, VHH,Single Domain Antibody
D018360	Crystallography, X-Ray	The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)	X-Ray Crystallography,Crystallography, X Ray,Crystallography, Xray,X Ray Crystallography,Xray Crystallography,Crystallographies, X Ray,X Ray Crystallographies
D020893	Receptor, ErbB-3	A cell surface protein-tyrosine kinase receptor that is specific for NEUREGULINS. It has extensive homology to and can heterodimerize with the EGF RECEPTOR and the ERBB-2 RECEPTOR. Overexpression of the erbB-3 receptor is associated with TUMORIGENESIS.	HER-3 Proto-Oncogene Protein,Proto-Oncogene Protein erbB-3,c-erbB-3 Protein,erbB-3 Protein,Proto-Oncogene Protein c-erbB-3,Proto-Oncogene Proteins erbB-3,Proto-oncogene-like Protein c-ErbB-2,Tyrosine Kinase-type Cell Surface Receptor HER3,ErbB-3 Receptor,HER 3 Proto Oncogene Protein,Protein c-ErbB-2, Proto-oncogene-like,Proto Oncogene Protein c erbB 3,Proto Oncogene Protein erbB 3,Proto Oncogene Proteins erbB 3,Proto oncogene like Protein c ErbB 2,Proto-Oncogene Protein, HER-3,Receptor, ErbB 3,Tyrosine Kinase type Cell Surface Receptor HER3,c erbB 3 Protein,c-ErbB-2, Proto-oncogene-like Protein,c-erbB-3, Proto-Oncogene Protein,erbB 3 Protein,erbB-3, Proto-Oncogene Protein,erbB-3, Proto-Oncogene Proteins