6PI7

Crystal structure of the TDRD2 extended Tudor domain in complex with an antibody fragment and the PIWIL1 peptide

Summary for 6PI7

• Entry DOI: 10.2210/pdb6pi7/pdb
• Descriptor: Tudor and KH domain-containing protein, Uncharacterized protein, Fab antigen-binding fragment, ... (5 entities in total)
• Functional Keywords: fab, tudor domain, piwil1, structural genomics, structural genomics consortium, sgc, protein binding
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 7
• Total formula weight: 153611.62

Authors

Liu, K.,Min, J.R.,Structural Genomics Consortium (SGC) (deposition date: 2019-06-26, release date: 2019-07-24, Last modification date: 2024-10-30)

Primary citation

Chen, S.,Zhang, W.,Min, J.,Liu, K.
Lesson from a Fab-enabled co-crystallization study of TDRD2 and PIWIL1.
Methods, 175:72-78, 2020

PubMed Abstract: The interaction of Tudor domain-containing proteins (TDRDs) with P-element-induced wimpy testis (PIWI) proteins plays critical roles in transposon silencing and spermatogenesis. Most human TDRDs recognize PIWI proteins in a methylarginine-dependent manner via their extended Tudor (eTudor) domains, except TDRD2, which prefers an unmethylated PIWI protein. In order to illustrate the recognition of unmethylated PIWI proteins by TDRD2, we extensively tried co-crystallization of the TDRD2 eTudor with different PIWIL1 peptides, but to no avail. Recombinant antigen-binding fragments (Fabs) have been used to crystallize some difficult proteins in the past, so we generated Fab against the TDRD2 eTudor protein using a phage-display antibody library, and one of these Fab fragments indeed facilitated the co-crystallization of TDRD2 and PIWIL1. Structural analysis of Fab, the TDRD2 eTudor domain in complex with an unmethylated PIWIL1-derived peptide revealed that the PIWIL1 residues G3 through R8 bound between the Tudor core and SN domain of TDRD2. The C-terminal residues of the PIWIL1 peptide were not resolved, presumably due to steric competition with the heavy chain of the Fab. We propose Fab-assisted crystallization as a tool not only for structural studies of single proteins, but also for analysis of interactions between proteins and their ligands in cases where co-crystallization of native protein complexes fails.

PubMed: 31288074
DOI: 10.1016/j.ymeth.2019.07.002

Experimental method

X-RAY DIFFRACTION (2.8 Å)