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F1000Research, volume 7, pages 57

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

Eliseev Igor E. ¹

Knyazev Nickolay A. ¹

Chakchir Oleg B. ¹

Vysochinskaya Vera V. ¹

Evstratyeva Anna V. ²

Drozhzhachih Maria S. ²

Krendeleva Elena A. ²

Vladimirova Anna K. ²

Nemankin Timofey A. ²

Ekimova Viktoria M. ²

Ulitin Andrey B. ²

Lomovskaya Maria I. ²

Yakovlev Pavel A. ²

Bukatin Anton S. ¹

Yudenko Anna N. ¹

Horak Sven ¹

Moiseenko Fedor V. ¹

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

CJSC Biocad, St. Petersburg, 198515, Russian Federation. |

Publication type: Journal Article

Publication date: 2018-07-04

F1000 Research

Journal: F1000Research

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ISSN: 20461402

DOI: 10.12688/f1000research.13612.2

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PubMed ID: 30430004

General Biochemistry, Genetics and Molecular Biology

General Medicine

General Immunology and Microbiology

General Pharmacology, Toxicology and Pharmaceutics

Abstract

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 KD=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.

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F1000Research	F1000Research, 1, 16.67% F1000Research 1 publication, 16.67%
Biomedicines	Biomedicines, 1, 16.67% Biomedicines 1 publication, 16.67%
Applied Microbiology and Biotechnology	Applied Microbiology and Biotechnology, 1, 16.67% Applied Microbiology and Biotechnology 1 publication, 16.67%
Protein Expression and Purification	Protein Expression and Purification, 1, 16.67% Protein Expression and Purification 1 publication, 16.67%
Methods in Enzymology	Methods in Enzymology, 1, 16.67% Methods in Enzymology 1 publication, 16.67%
Journal of Biological Chemistry	Journal of Biological Chemistry, 1, 16.67% Journal of Biological Chemistry 1 publication, 16.67%
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Elsevier	Elsevier, 2, 33.33% Elsevier 2 publications, 33.33%
F1000 Research	F1000 Research, 1, 16.67% F1000 Research 1 publication, 16.67%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 1, 16.67% Multidisciplinary Digital Publishing Institute (MDPI) 1 publication, 16.67%
Springer Nature	Springer Nature, 1, 16.67% Springer Nature 1 publication, 16.67%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 1, 16.67% American Society for Biochemistry and Molecular Biology 1 publication, 16.67%
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Eliseev I. E. et al. Crystal structures of a llama VHH antibody BCD090-M2 targeting human ErbB3 receptor // F1000Research. 2018. Vol. 7. p. 57.

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Vysochinskaya V. V., Chakchir O. B., Knyazev N. A., Bukatin A. S., Yakovlev P. A., Lomovskaya M. I., Ulitin A. B., Ekimova V. M., Nemankin T. A., Vladimirova A. K., Krendeleva E. A., Drozhzhachih M. S., Evstratyeva A. V., Eliseev I. E., Yudenko A. N., Horak S., Moiseenko F. V. Crystal structures of a llama VHH antibody BCD090-M2 targeting human ErbB3 receptor // F1000Research. 2018. Vol. 7. p. 57.

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TY - JOUR

DO - 10.12688/f1000research.13612.2

UR - https://doi.org/10.12688%2Ff1000research.13612.2

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

T2 - F1000Research

AU - Eliseev, Igor E.

AU - Vysochinskaya, Vera V.

AU - Evstratyeva, Anna V.

AU - Drozhzhachih, Maria S.

AU - Krendeleva, Elena A.

AU - Vladimirova, Anna K.

AU - Nemankin, Timofey A.

AU - Ekimova, Viktoria M.

AU - Ulitin, Andrey B.

AU - Lomovskaya, Maria I.

AU - Yakovlev, Pavel A.

AU - Bukatin, Anton S.

AU - Knyazev, Nickolay A.

AU - Chakchir, Oleg B.

AU - Yudenko, Anna N.

AU - Horak, Sven

AU - Moiseenko, Fedor V.

PY - 2018

DA - 2018/07/04 00:00:00

PB - F1000 Research

SP - 57

VL - 7

PMID - 30430004

SN - 2046-1402

ER -

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@article{2018_Eliseev,

author = {Igor E. Eliseev and Vera V. Vysochinskaya 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 Oleg B. Chakchir and Anna N. Yudenko and Sven Horak and Fedor V. Moiseenko},

title = {Crystal structures of a llama VHH antibody BCD090-M2 targeting human ErbB3 receptor},

journal = {F1000Research},

year = {2018},

volume = {7},

publisher = {F1000 Research},

month = {jul},

url = {https://doi.org/10.12688%2Ff1000research.13612.2},

pages = {57},

doi = {10.12688/f1000research.13612.2}

}

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F1000Research

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