1MM9

Streptavidin Mutant with Insertion of Fibronectin Hexapeptide, including RGD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization and comparison of RGD cell-adhesion recognition sites engineered into streptavidin.

Le Trong, I.McDevitt, T.C.Nelson, K.E.Stayton, P.S.Stenkamp, R.E.

(2003) Acta Crystallogr.,Sect.D 59: 828-834

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The RGD (arginine-glycine-aspartic acid) sequence is found in several important extracellular matrix proteins and serves as an adhesion ligand for members of the integrin family of cell-surface receptors. This sequence and flanking residues from fibr ...

    The RGD (arginine-glycine-aspartic acid) sequence is found in several important extracellular matrix proteins and serves as an adhesion ligand for members of the integrin family of cell-surface receptors. This sequence and flanking residues from fibronectin or osteopontin have been engineered into an accessible surface loop of streptavidin to create two new streptavidin variants (FN-SA or OPN-SA, respectively) that bind cells through the alpha(v)beta(3) and/or alpha(5)beta(1) integrin receptors. Their crystal structures confirm the design and construction of the mutants and provide evidence about the conformational dynamics of the RGD loops. The loops in the isomorphous crystal structures are involved in crystal-packing interactions and this stabilizes their structures. Even so, the loop in OPN-SA is slightly disordered and two of the residues are not seen in difference electron-density maps. Comparison with other experimentally determined structures of RGD loops in cell-adhesion molecules shows that these loops occupy a large subset of conformational space. This is consistent with the view that RGD loops, at least those involved in cell adhesion, sample a number of structures dynamically, a few of which display high affinity for appropriate receptors.


    Organizational Affiliation

    Department of Biological Structure, Biomolecular Structure Center, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Streptavidin
A
130Streptomyces avidinii
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.134 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.900α = 90.00
b = 56.900β = 90.00
c = 170.800γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance