2Z5O | pdb_00002z5o

Complex of Transportin 1 with JKTBP NLS

• PDB DOI: https://doi.org/10.2210/pdb2Z5O/pdb

• Classification: TRANSPORT PROTEIN/RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-07-14 Released: 2007-10-23 
• Deposition Author(s): Imasaki, T., Shimizu, T., Hashimoto, H., Hidaka, Y., Kose, S., Imamoto, N., Yamada, M., Sato, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.279 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Structural basis for substrate recognition and dissociation by human transportin 1

Imasaki, T., Shimizu, T., Hashimoto, H., Hidaka, Y., Kose, S., Imamoto, N., Yamada, M., Sato, M.

(2007) Mol Cell 28: 57-67

• PubMed: 17936704 
• DOI: https://doi.org/10.1016/j.molcel.2007.08.006
• Primary Citation Related Structures: 
  2Z5J, 2Z5K, 2Z5M, 2Z5N, 2Z5O


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 
• Field of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 102.28 kDa 
• Atom Count: 6,689 
• Modeled Residue Count: 844 
• Deposited Residue Count: 900 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transportin-1	A	890	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q92973 (Homo sapiens) Explore Q92973  Go to UniProtKB:  Q92973
PHAROS:  Q92973 GTEx:  ENSG00000083312

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterogeneous nuclear ribonucleoprotein D-like	B	10	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.279 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.306	α = 90
b = 169.805	β = 90
c = 68.458	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Imasaki, T., Shimizu, T., Hashimoto, H., Hidaka, Y., Kose, S., Imamoto, N., Yamada, M., Sato, M.

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description