Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104990.09 
• Atom Count: 6803 
• Residue Count: 920 
• Unique protein chains: 2

2Z5K

Complex of Transportin 1 with TAP NLS

• DOI: 10.2210/pdb2Z5K/pdb

• Classification: TRANSPORT PROTEIN/RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.268 
• R-Value Work: 0.221 

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: 10.1016/j.molcel.2007.08.006
• Primary Citation of Related Structures:  
  2Z5O, 2Z5N, 2Z5M, 2Z5J


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Transportin-1	A	890	Homo sapiens	Mutation(s): 0  Gene Names: TNPO1 (KPNB2, MIP1, TRN)
Find proteins for Q92973 (Homo sapiens) Go to Gene View: TNPO1 Go to UniProtKB:  Q92973

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Nuclear RNA export factor 1	B	30	Homo sapiens	Mutation(s): 0  Gene Names: NXF1 (TAP)
Find proteins for Q9UBU9 (Homo sapiens) Go to Gene View: NXF1 Go to UniProtKB:  Q9UBU9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.268 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 69.643	α = 90.00
b = 119.737	β = 90.00
c = 147.853	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History 

• Version 1.0: 2007-10-23
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.2: 2018-05-09
  Type: Advisory, Data collection, Derived calculations, Source and taxonomy