PDBsum entry 1o6p

Nuclear transport

PDB id: 1o6p

Contents

Protein chain

441 a.a. *

Ligands

GLY-LEU-PHE-GLY-SER ×2

LEU-PHE-GLY-SER ×2

Waters ×36

* Residue conservation analysis

PDB id:

1o6p

Name:

Nuclear transport

Title:

Importin beta bound to a glfg nucleoporin peptide

Structure:

Importin beta-1 subunit. Chain: a, b. Fragment: importin beta-1 subunit, residues 1-442. Synonym: karyopherin beta-1 subunit, nuclear factor p97, importin 90, kpnb1, ntf97. Engineered: yes. Synthetic glfg peptide. Chain: c, d, e, f. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Biol. unit:

Trimer (from PDB file)

Resolution:

2.80Å R-factor: 0.238 R-free: 0.267

Authors:

R.Bayliss,M.Stewart

Key ref:

R.Bayliss et al. (2002). GLFG and FxFG nucleoporins bind to overlapping sites on importin-beta. J Biol Chem, 277, 50597-50606. PubMed id: 12372823 DOI: 10.1074/jbc.M209037200

Date:

10-Oct-02 Release date: 24-Apr-03

Protein chains

Q14974  (IMB1_HUMAN) -  Importin subunit beta-1 from Homo sapiens

Seq: 876 a.a.

Struc: 441 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.M209037200

J Biol Chem 277:50597-50606 (2002)

PubMed id: 12372823

GLFG and FxFG nucleoporins bind to overlapping sites on importin-beta.

R.Bayliss, T.Littlewood, L.A.Strawn, S.R.Wente, M.Stewart.

ABSTRACT

The interaction between nuclear pore proteins (nucleoporins) and transport factors is crucial for the translocation of macromolecules through nuclear pores. Many nucleoporins contain FG sequence repeats, and previous studies have demonstrated interactions between repeats containing FxFG or GLFG cores and transport factors. The crystal structure of residues 1-442 of importin-beta bound to a GLFG peptide indicates that this repeat core binds to the same primary site as FxFG cores. Importin-beta-I178D shows reduced binding to both FxFG and GLFG repeats, consistent with both binding to an overlapping site in the hydrophobic groove between the A-helices of HEAT repeats 5 and 6. Moreover, FxFG repeats can displace importin-beta or its S. cerevisiae homologue, Kap95, bound to GLFG repeats. Addition of soluble GLFG repeats decreases the rate of nuclear protein import in digitonin-permeabilized HeLa cells, indicating that this interaction has a role in the translocation of carrier-cargo complexes through nuclear pores. The binding of GLFG and FxFG repeats to overlapping sites on importin-beta indicates that functional differences between different repeats probably arise from differences in their spatial organization.

Selected figure(s)

Figure 1.
Fig. 1. Binding of GLFG and FxFG repeats to Ib442. Annealed omit F[o] F[c] maps contoured at 2.5 at the primary GLFG binding site (A) (site 1, see C) and the primary FxFG binding site (B). C, the GLFG peptide showed difference density located at two sites on Ib442. Site 1 (black) was located between the A-helices of HEAT repeats 5 and 6 and was also the primary site at which FxFG cores bound, whereas site 2 (red) was located at a contact between two Ib442 chains in the crystal and was thought to be a crystallization artifact.

Figure 2.
Fig. 2. Details of the interaction between GLFG and FxFG cores and Ib442. Stereo views of GLFG (A, black) and FxFG (B, red) cores show that each binds in the hydrophobic pocket (yellow) formed between HEAT repeats 5 (light green) and 6 (light blue) by the side chains of Leu174, Thr175, Ile^178, Glu214, Phe^217, and Ile^218. In addition to the hydrophobic interaction, putative H-bonds are formed between the main chain and Glu214. Thr175 forms a H-bond to the FxFG core but not to the GLFG core. Surface views (D and E) illustrate the intimacy of the contact between the repeat cores and Ib442. In contrast, the contact between the GLFG peptide at site 2 involved a pocket formed by two Ib442 chains (green and orange in C and F) and neither Ib442 chain alone buried a significant amount of the core, consistent with site 2 representing a crystallization artifact and site 1 representing the true GLFG binding site. G, although the conformation of GLFG and FxFG cores bound to Ib442 was different, they had a similar outline.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 50597-50606) copyright 2002.

Figures were selected by an automated process.