4EIK

Crystal Structure of the Human Fyn SH3 domain in complex with the synthetic peptide VSL12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallization of and selenomethionine phasing strategy for a SETMAR-DNA complex.

Chen, Q.Georgiadis, M.

(2016) Acta Crystallogr F Struct Biol Commun 72: 713-719

  • DOI: 10.1107/S2053230X16012723

  • PubMed Abstract: 
  • Transposable elements have played a critical role in the creation of new genes in all higher eukaryotes, including humans. Although the chimeric fusion protein SETMAR is no longer active as a transposase, it contains both the DNA-binding domain (DBD) ...

    Transposable elements have played a critical role in the creation of new genes in all higher eukaryotes, including humans. Although the chimeric fusion protein SETMAR is no longer active as a transposase, it contains both the DNA-binding domain (DBD) and catalytic domain of the Hsmar1 transposase. The amino-acid sequence of the DBD has been virtually unchanged in 50 million years and, as a consequence, SETMAR retains its sequence-specific binding to the ancestral Hsmar1 terminal inverted repeat (TIR) sequence. Thus, the DNA-binding activity of SETMAR is likely to have an important biological function. To determine the structural basis for the recognition of TIR DNA by SETMAR, the design of TIR-containing oligonucleotides and SETMAR DBD variants, crystallization of DBD-DNA complexes, phasing strategies and initial phasing experiments are reported here. An unexpected finding was that oligonucleotides containing two BrdUs in place of thymidines produced better quality crystals in complex with SETMAR than their natural counterparts.


    Organizational Affiliation

    Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase Fyn
A
64Homo sapiensMutation(s): 0 
Gene Names: FYN
EC: 2.7.10.2
Find proteins for P06241 (Homo sapiens)
Go to Gene View: FYN
Go to UniProtKB:  P06241
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VSL12 peptide
B
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 81.843α = 90.00
b = 81.843β = 90.00
c = 35.904γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
ADSCdata collection
SCALAdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-04-05 
  • Released Date: 2013-04-10 
  • Deposition Author(s): Camara-Artigas, A.

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description
  • Version 1.3: 2018-04-18
    Type: Data collection, Database references