PDBsum entry 2z5n

Go to PDB code: 
protein Protein-protein interface(s) links
Transport protein/RNA binding protein PDB id
Jmol PyMol
Protein chains
840 a.a. *
15 a.a. *
* Residue conservation analysis
PDB id:
Name: Transport protein/RNA binding protein
Title: Complex of transportin 1 with hnrnp d nls
Structure: Transportin-1. Chain: a. Synonym: importin beta-2, karyopherin beta-2, m9 region int protein, mip. Engineered: yes. Heterogeneous nuclear ribonucleoprotein d0. Chain: b. Fragment: c-terminal domain, unp residues 332-355. Synonym: hnrnp d0, au-rich element RNA-binding protein 1, h
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: chemical synthesis. This sequence occurs nat humans.
3.20Å     R-factor:   0.235     R-free:   0.295
Authors: T.Imasaki,T.Shimizu,H.Hashimoto,Y.Hidaka,S.Kose,N.Imamoto,M. M.Sato
Key ref:
T.Imasaki et al. (2007). Structural basis for substrate recognition and dissociation by human transportin 1. Mol Cell, 28, 57-67. PubMed id: 17936704 DOI: 10.1016/j.molcel.2007.08.006
14-Jul-07     Release date:   23-Oct-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q92973  (TNPO1_HUMAN) -  Transportin-1
898 a.a.
840 a.a.
Protein chain
Pfam   ArchSchema ?
Q14103  (HNRPD_HUMAN) -  Heterogeneous nuclear ribonucleoprotein D0
355 a.a.
15 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cilium   7 terms 
  Biological process     viral reproduction   9 terms 
  Biochemical function     protein binding     5 terms  


DOI no: 10.1016/j.molcel.2007.08.006 Mol Cell 28:57-67 (2007)
PubMed id: 17936704  
Structural basis for substrate recognition and dissociation by human transportin 1.
T.Imasaki, T.Shimizu, H.Hashimoto, Y.Hidaka, S.Kose, N.Imamoto, M.Yamada, M.Sato.
Transportin 1 (Trn1) is a transport receptor that transports substrates from the cytoplasm to the nucleus through nuclear pore complexes by recognizing nuclear localization signals (NLSs). Here we describe four crystal structures of human Trn1 in a substrate-free form as well as in the complex with three NLSs (hnRNP D, JKTBP, and TAP, respectively). Our data have revealed that (1) Trn1 has two sites for binding NLSs, one with high affinity (site A) and one with low affinity (site B), and NLS interaction at site B controls overall binding affinity for Trn1; (2) Trn1 recognizes the NLSs at site A followed by conformational change at site B to interact with the NLSs; and (3) a long flexible loop, characteristic of Trn1, interacts with site B, thereby displacing transport substrate in the nucleus. These studies provide deep understanding of substrate recognition and dissociation by Trn1 in import pathways.
  Selected figure(s)  
Figure 3.
Figure 3. NLS Recognition by Trn1
(A) Schematic illustrations of Trn1 interactions with hnRNP D NLS (left) and TAP NLS (right). Trn1-NLS contacts less than 3.8 Å are shown. HEAT repeats 8–13 correspond to site A, and HEAT repeats 14–18 to site B.
(B) Structures of hnRNP D NLS (green), TAP NLS (blue), hnRNP A1 NLS (orange), and hnRNP M NLS (purple) bound to Trn1. Two close-up views of the structures at the right side and one close-up view at the left side show the interactions with Trn1 at sites A and B, respectively. Structures of hnRNP A1 NLS and hnRNP M NLS bound to an H8 loop-truncated Trn1 mutant were drawn with the refined coordinates deposited in the Protein Data Bank (accession codes 2H4M and 2OT8).
Figure 6.
Figure 6. Schematic Illustration of a Proposed Mechanism for the Nuclear Import Pathway Mediated by Trn1
The Trn1 molecule is represented by the S-like cyan ribbon labeled with N and C termini. NPC is the nuclear pore complex. Red and blue ellipsoids on the NLS in transport substrate show the three consensus residues (red ellipsoid) and one hydrophobic residue (blue ellipsoid).
  The above figures are reprinted by permission from Cell Press: Mol Cell (2007, 28, 57-67) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21139563 M.Grünwald, and F.Bono (2011).
Structure of Importin13-Ubc9 complex: nuclear import and release of a key regulator of sumoylation.
  EMBO J, 30, 427-438.
PDB code: 2xwu
20606625 D.Dormann, R.Rodde, D.Edbauer, E.Bentmann, I.Fischer, A.Hruscha, M.E.Than, I.R.Mackenzie, A.Capell, B.Schmid, M.Neumann, and C.Haass (2010).
ALS-associated fused in sarcoma (FUS) mutations disrupt Transportin-mediated nuclear import.
  EMBO J, 29, 2841-2857.  
20421341 L.Chen, C.Shao, E.Cobos, J.S.Wang, and W.Gao (2010).
4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone [corrected] induces CRM1-dependent p53 nuclear accumulation in human bronchial epithelial cells.
  Toxicol Sci, 116, 206-215.  
19124778 J.C.Phillips (2009).
Scaling and self-organized criticality in proteins II.
  Proc Natl Acad Sci U S A, 106, 3113-3118.  
19124606 J.Fritz, A.Strehblow, A.Taschner, S.Schopoff, P.Pasierbek, and M.F.Jantsch (2009).
RNA-regulated interaction of transportin-1 and exportin-5 with the double-stranded RNA-binding domain regulates nucleocytoplasmic shuttling of ADAR1.
  Mol Cell Biol, 29, 1487-1497.  
18532879 K.E.Süel, H.Gu, and Y.M.Chook (2008).
Modular organization and combinatorial energetics of proline-tyrosine nuclear localization signals.
  PLoS Biol, 6, e137.  
18846510 N.Favre, M.Camps, C.Arod, C.Chabert, C.Rommel, and C.Pasquali (2008).
Chemokine receptor CCR2 undergoes transportin1-dependent nuclear translocation.
  Proteomics, 8, 4560-4576.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.