Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 8.51 kDa 
• Atom Count: 602 
• Modelled Residue Count: 69 
• Deposited Residue Count: 76 
• Unique protein chains: 2

4EIK

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

• PDB DOI: 10.2210/pdb4EIK/pdb

• Classification: TRANSFERASE/PROTEIN BINDING
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.195 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

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

• PubMed: 27599863 
• DOI: 10.1107/S2053230X16012723
• Primary Citation of Related Structures:  
  4EIK


• 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 Although the chimeric fusion protein SETMAR is no longer active as a transposase, it contains both the DNA-binding domain (DBD) and catalytic domain of the Hsmar1 transposase.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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Fyn	A	64	Homo sapiens	Mutation(s): 0  Gene Names: FYN EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06241 (Homo sapiens) Explore P06241  Go to UniProtKB:  P06241
PHAROS:  P06241

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VSL12 peptide	B	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.195 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.843	α = 90
b = 81.843	β = 90
c = 35.904	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2018-04-18
  Changes: Data collection, Database references