1SJV

Three-Dimensional Structure of a Llama VHH Domain Swapping

Summary for 1SJV

• Entry DOI: 10.2210/pdb1sjv/pdb
• Descriptor: r9 (2 entities in total)
• Functional Keywords: camelids antibody, domain swapping, heavy chain antibody, antibiotic
• Biological source: Lama glama (llama)
• Total number of polymer chains: 1
• Total formula weight: 12640.01

Authors

Spinelli, S.,Desmyter, A.,Frenken, L.,Verrips, T.,Cambillau, C. (deposition date: 2004-03-04, release date: 2004-06-01, Last modification date: 2024-10-30)

Primary citation

Spinelli, S.,Desmyter, A.,Frenken, L.,Verrips, T.,Tegoni, M.,Cambillau, C.
Domain swapping of a llama VHH domain builds a crystal-wide beta-sheet structure.
Febs Lett., 564:35-40, 2004

PubMed Abstract: Among mammals, camelids have a unique immunological system since they produce functional antibodies devoid of light chains and CH1 domains. To bind antigens, whether they are proteins or haptens, camelids use the single domain VH from their heavy chain (VHH). We report here on such a llama VHH domain (VHH-R9) which was raised against a hapten, the RR6 red dye. This VHH possesses the shortest complementarity determining region 3 (CDR3) among all the known VHH sequences and nevertheless binds RR6 efficiently with a K(d) value of 83 nM. However, the crystal structure of VHH-R9 exhibits a striking feature: its CDR3 and its last beta-strand (beta9) do not follow the immunoglobulin VH domain fold, but instead extend out of the VHH molecular boundary and associate with a symmetry-related molecule. The two monomers thus form a domain-swapped dimer which establishes further contacts with symmetry-related molecules and build a crystal-wide beta-sheet structure. The driving force of the dimer formation is probably the strain induced by the short CDR3 together with the cleavage of the first seven residues.

PubMed: 15094039
DOI: 10.1016/S0014-5793(04)00304-7

Experimental method

X-RAY DIFFRACTION (1.94 Å)