2R8S

High resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain

Summary for 2R8S

• Entry DOI: 10.2210/pdb2r8s/pdb
• Descriptor: P4-P6 RNA RIBOZYME DOMAIN, Fab light chain, Fab heavy chain, ... (5 entities in total)
• Functional Keywords: protein-rna complex, fab-rna complex, immune system-rna complex, immune system/rna
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 3
• Total formula weight: 98454.99

Authors

Ye, J.D.,Tereshko, V.,Sidhu, S.S.,Koide, S.,Kossiakoff, A.A.,Piccirilli, J.A. (deposition date: 2007-09-11, release date: 2007-12-04, Last modification date: 2024-10-30)

Primary citation

Ye, J.D.,Tereshko, V.,Frederiksen, J.K.,Koide, A.,Fellouse, F.A.,Sidhu, S.S.,Koide, S.,Kossiakoff, A.A.,Piccirilli, J.A.
Synthetic antibodies for specific recognition and crystallization of structured RNA
Proc.Natl.Acad.Sci.Usa, 105:82-87, 2008

PubMed Abstract: Antibodies that bind protein antigens are indispensable in biochemical research and modern medicine. However, knowledge of RNA-binding antibodies and their application in the ever-growing RNA field is lacking. Here we have developed a robust approach using a synthetic phage-display library to select specific antigen-binding fragments (Fabs) targeting a large functional RNA. We have solved the crystal structure of the first Fab-RNA complex at 1.95 A. Capability in phasing and crystal contact formation suggests that the Fab provides a potentially valuable crystal chaperone for RNA. The crystal structure reveals that the Fab achieves specific RNA binding on a shallow surface with complementarity-determining region (CDR) sequence diversity, length variability, and main-chain conformational plasticity. The Fab-RNA interface also differs significantly from Fab-protein interfaces in amino acid composition and light-chain participation. These findings yield valuable insights for engineering of Fabs as RNA-binding modules and facilitate further development of Fabs as possible therapeutic drugs and biochemical tools to explore RNA biology.

PubMed: 18162543
DOI: 10.1073/pnas.0709082105

Experimental method

X-RAY DIFFRACTION (1.95 Å)