3GJ7

Crystal structure of human RanGDP-Nup153ZnF12 complex

Summary for 3GJ7

• Entry DOI: 10.2210/pdb3gj7/pdb
• Related: 1BYU 2GQE 3CH5 3GJ0 3GJ3 3GJ4 3GJ5 3GJ6 3GJ8
• Descriptor: GTP-binding nuclear protein Ran, Nuclear pore complex protein Nup153, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: g protein, gdp, ran, nup153, nuclear pore, zinc finger, acetylation, cytoplasm, gtp-binding, host-virus interaction, isopeptide bond, nucleotide-binding, nucleus, phosphoprotein, polymorphism, protein transport, transport, ubl conjugation, dna-binding, metal-binding, mrna transport, nuclear pore complex, translocation, zinc, zinc-finger, transport protein
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P62826; Nucleus, nuclear pore complex: P49791
• Total number of polymer chains: 4
• Total formula weight: 71143.13

Authors

Partridge, J.R.,Schwartz, T.U. (deposition date: 2009-03-07, release date: 2009-08-04, Last modification date: 2023-09-06)

Primary citation

Partridge, J.R.,Schwartz, T.U.
Crystallographic and Biochemical Analysis of the Ran-binding Zinc Finger Domain.
J.Mol.Biol., 391:375-389, 2009

PubMed Abstract: The nuclear pore complex (NPC) resides in circular openings within the nuclear envelope and serves as the sole conduit to facilitate nucleocytoplasmic transport in eukaryotes. The asymmetric distribution of the small G protein Ran across the nuclear envelope regulates directionality of protein transport. Ran interacts with the NPC of metazoa via two asymmetrically localized components, Nup153 at the nuclear face and Nup358 at the cytoplasmic face. Both nucleoporins contain a stretch of distinct, Ran-binding zinc finger domains. Here, we present six crystal structures of Nup153-zinc fingers in complex with Ran and a 1.48 A crystal structure of RanGDP. Crystal engineering allowed us to obtain well diffracting crystals so that all ZnF-Ran complex structures are refined to high resolution. Each of the four zinc finger modules of Nup153 binds one Ran molecule in apparently non-allosteric fashion. The affinity is measurably higher for RanGDP than for RanGTP and varies modestly between the individual zinc fingers. By microcalorimetric and mutational analysis, we determined that one specific hydrogen bond accounts for most of the differences in the binding affinity of individual zinc fingers. Genomic analysis reveals that only in animals do NPCs contain Ran-binding zinc fingers. We speculate that these organisms evolved a mechanism to maintain a high local concentration of Ran at the vicinity of the NPC, using this zinc finger domain as a sink.

PubMed: 19505478
DOI: 10.1016/j.jmb.2009.06.011

Experimental method

X-RAY DIFFRACTION (1.93 Å)