3CFI

Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus

Summary for 3CFI

• Entry DOI: 10.2210/pdb3cfi/pdb
• Descriptor: Type II secretory pathway, pseudopilin EpsI, Type II secretory pathway, PSEUDOPILIN EpsJ, Nanobody NBEPSIJ_11, ... (5 entities in total)
• Functional Keywords: general secretory pathway, pseudopilins, single chain antibody, methylation, protein transport-immune system complex, protein transport/immune system
• Biological source: Vibrio vulnificus; More
• Total number of polymer chains: 12
• Total formula weight: 164319.11

Authors

Lam, A.Y.,Pardon, E.,Korotkov, K.V.,Steyaert, J.,Hol, W.G.J. (deposition date: 2008-03-03, release date: 2009-01-13, Last modification date: 2024-11-20)

Primary citation

Lam, A.Y.,Pardon, E.,Korotkov, K.V.,Hol, W.G.,Steyaert, J.
Nanobody-aided structure determination of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus.
J.Struct.Biol., 166:8-15, 2009

PubMed Abstract: Pseudopilins form the central pseudopilus of the sophisticated bacterial type 2 secretion systems. The crystallization of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus was greatly accelerated by the use of nanobodies, which are the smallest antigen-binding fragments derived from heavy-chain only camelid antibodies. Seven anti-EpsI:EpsJ nanobodies were generated and co-crystallization of EpsI:EpsJ nanobody complexes yielded several crystal forms very rapidly. In the structure solved, the nanobodies are arranged in planes throughout the crystal lattice, linking layers of EpsI:EpsJ heterodimers. The EpsI:EpsJ dimer observed confirms a right-handed architecture of the pseudopilus, but, compared to a previous structure of the EpsI:EpsJ heterodimer, EpsI differs 6 degrees in orientation with respect to EpsJ; one loop of EpsJ is shifted by approximately 5A due to interactions with the nanobody; and a second loop of EpsJ underwent a major change of 17A without contacts with the nanobody. Clearly, nanobodies accelerate dramatically the crystallization of recalcitrant protein complexes and can reveal conformational flexibility not observed before.

PubMed: 19118632
DOI: 10.1016/j.jsb.2008.11.008

Experimental method

X-RAY DIFFRACTION (2.58 Å)