Structural Biology and Regulation of Protein Import into the Nucleus

TLDR: The structural basis of the principal nuclear import pathways and the molecular basis of their regulation are reviewed and post-translational modifications, particularly phosphorylation, constitute key regulatory mechanisms operating in these pathways.

About: This article is published in Journal of Molecular Biology.The article was published on 2016-05-22 and is currently open access. It has received 195 citations till now. The article focuses on the topics: Nuclear transport & Nuclear protein.

Figures

Fig. 3. Structures of (A) Ran:RanBD1:Impβ1(1–462) [32] and 1K5D). RanBD1 forms a molecular embrace with Ran, seques RanGTP-Impβ structure onto the ternary complexes reveals ste

Fig. 6. Structures of Imp13. PDB entries: Mago-Y14 complex (2X1G), UBC9 complex (2XWU), Ran complex (2X19) and apo (3ZKV). The HEAT repeats involved in cargo binding are highlighted in dark yellow. A representative Imp13 from Imp13:Ran complex has all cargoes overlaid.

Fig. 1. Overview of the main nuclear import pathways. Schematic illustration of three different nuclear import pathways. (i and ii) Classic import pathway; cargo (nucleoplasmin, shown in red; PDB entry 1K5J), Impα (shown in green; PDB entries 1IAL and 1EE5) and Impβ1 (shown in yellow; PDB entry 1QGK) form a ternary complex before translocating across the membrane via the nuclear pore (shown in gray); RanGTP (shown in blue; PDB entry 2BKU) and Cse1p [or CAS] (shown in orange; PDB entry 1WA5) dissociate the complex and release the cargo. (iii and iv) Snurportin-1 import pathway; cargo (U1A-UTR, shown in red and wheat; PDB entry 1AUD), snurportin-1 (shown in green; PDB entry 1UKL) and Impβ1 translocate across the membrane; RanGTP and CRM1 (shown in orange; PDB entry 3GJX) release the cargo. (v and vi) Import pathway involving direct cargo binding to Impβ1; cargo (SREBP2, shown in red; PDB entry 1UKL) and Impβ1 form a binary complex before translocating across the membrane; RanGTP dissociates the complex.

Fig. 5. Structures of Trn3. PDB entries: ASF/SF2 complex (4C0O), Ran complex (4C0Q) and apo (4C0P). The HEAT repeats involved in cargo binding are highlighted in dark yellow. A representative Trn3 in apo-form has all cargoes overlaid.

Table 1. Structurally characterized transport receptors involve

Fig. 9. NTF2 dimer (blue) bound to two chains of RanGDP (green) and two FxFG Nup motif cores (yellow) (based on PDB entries 5BXQ and 1GYB). (A) The two chains of the NTF2 dimer interact through an extensive β-sheet, whereas the remainder of the molecule generates a cavity into which Phe72 of the RanGDP switch-II loop binds. The FxFG motif cores bind in a hydrophobic cavity generated between the two NTF2 chains. (B) Binding of the RanGDP switch-II loop to NTF2. Ran Phe72 inserts into the hydrophobic cavity and is supplemented by salt bridges formedbetween Lys71 andArg76 of RanandAsp92/94 and Glu42 of NTF2, respectively.

Frequently asked questions

Q1. What is the structure of the RS domain of ASF/SF2?

Residues within HEAT repeat 15, particularly Arg-rich regions within B-helices, are the key binding determinants for the recognition of the phosphorylated RS domain of ASF/SF2 [58]. 

Q2. What is the third site of the yImp1 binder?

The third site, where theRanGTPswitchI loop binds theC-terminal arch of yImpβ1, is crucial for locking the molecule in a conformation with increased curvature that cannot bind cargo. 

Q3. What is the first interacting region of the molecule?

The first interacting region involves hydrophobic interactions mediated by a loop and a helix that bind both helices within HEAT repeat 1 and the B-helix of HEAT repeat 2 of Imp13. 

Q4. How many residues are required to allow functional cNLSs to interact with the Imp?

Structural studies showed that a minimum of 10 residues between the P2′ and P2 positions is required to allow functional cNLSs to interact simultaneously with both the major and minor binding sites on the Impα surface [56]. 

Q5. How does Imp1 bind to HEAT repeats?

To bind four zinc finger domains (ZF) of Snail1 (residues 151–264), Impβ1 uses the B-helices of HEAT repeats 5–14, including the acidic loop in HEAT repeat 8. 

Q6. How does Snail1 bind to HEAT repeats?

Snail1 binds through 15 intermolecular interactions in the B-helices of HEAT repeats 5–14 that bury 2205 Å2 of surface area [25]. 

Q7. Where do the HEAT repeats 8 and 9 interact with the Mago -sheet?

HEAT repeats 8 and 9 interact with the Mago β-sheet, at the site where the N terminal region of Y14 is bound, and HEAT repeat15 binds at the opposite side of the Mago β-sheet. 

Q8. What is the size of the yImp1:RanGTP interface?

The size of the yImpβ1:RanGTP interface (2159 Å2 [28]) is similar to the interfaces found in cargo and adaptor complexes, and there is limited overlap between the binding sites. 

Q9. What is the role of Arg and Lys in cNLS cargoes?

cNLS cargoes are defined by the presence of one or two sequence clusters rich in Arg and Lys that are necessary and sufficient for nuclear import by the Impα:Impβ1 complex. 

Q10. What is the only organism for which the structures of different Imp variants are available?

The human is the only organism for which the structures of different Impα variants are available [83–85,113,126] (Supplementary Table 3). 

Q11. Why do some proteins have a large repertoire of nuclear import receptors?

The reason for the large repertoire of nuclear import receptors within cells remains to be fully elucidated; in part, it can be attributed to the requirement of cells to translocate hundreds of quite disparate macromolecules across the nuclear envelope. 

Q12. What is the role of the minor binding site in the 1-like Imp family?

The minor binding site may play a more important role in the α1-like Impα family, which includes the rice and N. crassa proteins.