5B5G

Crystal structure of ALiS4-Streptavidin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Improving the Solubility of Artificial Ligands of Streptavidin to Enable More Practical Reversible Switching of Protein Localization in Cells

Tachibana, R.Terai, T.Boncompain, G.Sugiyama, S.Saito, N.Perez, F.Urano, Y.

(2017) Chembiochem 18: 358-362

  • DOI: 10.1002/cbic.201600640
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chemical inducers that can control target-protein localization in living cells are powerful tools to investigate dynamic biological systems. We recently reported the retention using selective hook or "RUSH" system for reversible localization change o ...

    Chemical inducers that can control target-protein localization in living cells are powerful tools to investigate dynamic biological systems. We recently reported the retention using selective hook or "RUSH" system for reversible localization change of proteins of interest by addition/washout of small-molecule artificial ligands of streptavidin (ALiS). However, the utility of previously developed ALiS was restricted by limited solubility in water. Here, we overcame this problem by X-ray crystal structure-guided design of a more soluble ALiS derivative (ALiS-3), which retains sufficient streptavidin-binding affinity for use in the RUSH system. The ALiS-3-streptavidin interaction was characterized in detail. ALiS-3 is a convenient and effective tool for dynamic control of α-mannosidase II localization between ER and Golgi in living cells.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Streptavidin
A, B, C, D
120Streptomyces avidiniiMutation(s): 0 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6FX
Query on 6FX

Download SDF File 
Download CCD File 
C, D
methyl 5-(4-oxidanylidene-5~{H}-furo[3,2-c]pyridin-2-yl)pyridine-3-carboxylate
methyl 5-(4-oxo-4,5-dihydrofuro[3,2-c]pyridin-2-yl)nicotinate
C14 H10 N2 O4
CKTWBGKZILYBCF-UHFFFAOYSA-N
 Ligand Interaction
SO3
Query on SO3

Download SDF File 
Download CCD File 
A, B, C, D
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6FXKd: 5600 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.921α = 90.00
b = 84.423β = 98.98
c = 46.138γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KAKENHIJapan25286051
JSPS KAKENHIJapan25650051
JSPS KAKENHIJapan23860028

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release