4Y59 | pdb_00004y59

Crystal structure of ALiS1-Streptavidin complex

• PDB DOI: https://doi.org/10.2210/pdb4Y59/pdb

• Classification: BIOTIN-Binding protein
• Organism(s): Streptomyces avidinii
• Expression System: Streptomyces avidinii
• Mutation(s): No 


• Deposited: 2015-02-11 Released: 2015-09-23 
• Deposition Author(s): Sugiyama, S., Terai, T., Kohno, M., Ishida, H., Nagano, T.
• Funding Organization(s): JSPS KAKENHI (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.155 (Depositor), 0.157 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.127 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Literature

Artificial Ligands of Streptavidin (ALiS): Discovery, Characterization, and Application for Reversible Control of Intracellular Protein Transport

Terai, T., Kohno, M., Boncompain, G., Sugiyama, S., Saito, N., Fujikake, R., Ueno, T., Komatsu, T., Hanaoka, K., Okabe, T., Urano, Y., Perez, F., Nagano, T.

(2015) J Am Chem Soc 137: 10464-10467

• PubMed: 26261872 
• DOI: https://doi.org/10.1021/jacs.5b05672
• Primary Citation Related Structures: 
  4Y59, 4Y5D


• PubMed Abstract: 
  

  Artificial ligands of streptavidin (ALiS) with association constants of ∼10(6) M(-1) were discovered by high-throughput screening of our chemical library, and their binding characteristics, including X-ray crystal structure of the streptavidin complex, were determined. Unlike biotin and its derivatives, ALiS exhibits fast dissociation kinetics and excellent cell permeability. The streptavidin-ALiS system provides a novel, practical compound-dependent methodology for repeated reversible cycling of protein localization between intracellular organella.

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Organizational Affiliation: 
• Graduate School of Science, Osaka University , 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 52.18 kDa 
• Atom Count: 4,413 
• Modeled Residue Count: 484 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	121	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T21	E [auth A], F [auth B], G [auth C], H [auth D]	2-[3-(trifluoromethyl)phenyl]furo[3,2-c]pyridin-4(5H)-one C14 H8 F3 N O2 ICVXPLDIRPNIOG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.155 (Depositor), 0.157 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.127 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.843	α = 90
b = 84.353	β = 98.92
c = 46.156	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Sugiyama, S., Terai, T., Kohno, M., Ishida, H., Nagano, T.

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Funding Organization	Location	Grant Number
JSPS KAKENHI (Japan)	Japan	25286051
JSPS KAKENHI (Japan)	Japan	25650051

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2015-12-16
  Changes: Database references
• Version 1.2: 2020-02-05
  Changes: Data collection, Derived calculations
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references