2KTR

NMR structure of p62 PB1 dimer determined based on PCS

Summary for 2KTR

• Entry DOI: 10.2210/pdb2ktr/pdb
• Related: 2KKC 2RPV
• Descriptor: Sequestosome-1, TERBIUM(III) ION (3 entities in total)
• Functional Keywords: autophagy, nf-kb signaling, homo-oligomer, pb1 dimer, signaling protein, transport protein
• Biological source: Rattus norvegicus (Rat); More
• Cellular location: Cytoplasm: O08623 O08623
• Total number of polymer chains: 2
• Total formula weight: 24391.13

Authors

Saio, T.,Yokochi, M.,Kumeta, H.,Inagaki, F. (deposition date: 2010-02-05, release date: 2010-04-07, Last modification date: 2024-05-29)

Primary citation

Saio, T.,Yokochi, M.,Kumeta, H.,Inagaki, F.
PCS-based structure determination of protein-protein complexes
J.Biomol.Nmr, 46:271-280, 2010

PubMed Abstract: A simple and fast nuclear magnetic resonance method for docking proteins using pseudo-contact shift (PCS) and (1)H(N)/(15)N chemical shift perturbation is presented. PCS is induced by a paramagnetic lanthanide ion that is attached to a target protein using a lanthanide binding peptide tag anchored at two points. PCS provides long-range (approximately 40 A) distance and angular restraints between the lanthanide ion and the observed nuclei, while the (1)H(N)/(15)N chemical shift perturbation data provide loose contact-surface information. The usefulness of this method was demonstrated through the structure determination of the p62 PB1-PB1 complex, which forms a front-to-back 20 kDa homo-oligomer. As p62 PB1 does not intrinsically bind metal ions, the lanthanide binding peptide tag was attached to one subunit of the dimer at two anchoring points. Each monomer was treated as a rigid body and was docked based on the backbone PCS and backbone chemical shift perturbation data. Unlike NOE-based structural determination, this method only requires resonance assignments of the backbone (1)H(N)/(15)N signals and the PCS data obtained from several sets of two-dimensional (15)N-heteronuclear single quantum coherence spectra, thus facilitating rapid structure determination of the protein-protein complex.

PubMed: 20300805
DOI: 10.1007/s10858-010-9401-4

Experimental method

SOLUTION NMR