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 
  • R-Value Observed: 0.145 

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 D Biol Crystallogr 59: 828-834

  • DOI: 10.1107/s0907444903004153
  • Primary Citation of Related Structures:  
    1MM9, 1MOY

  • 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 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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
StreptavidinA130Streptomyces avidiniiMutation(s): 0 
Gene Names: core streptavidin
Membrane Entity: Yes 
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22629
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download Ideal Coordinates CCD File 
B [auth A],
C [auth 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 
  • R-Value Observed: 0.145 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.9α = 90
b = 56.9β = 90
c = 170.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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