6NMW

Crystal structure of the human Lyn SH3 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the SH3 domain of human Lyn non-receptor tyrosine kinase.

Berndt, S.Gurevich, V.V.Iverson, T.M.

(2019) PLoS One 14: e0215140-e0215140

  • DOI: 10.1371/journal.pone.0215140
  • Primary Citation of Related Structures:  
    6NMW

  • PubMed Abstract: 
  • Lyn kinase (Lck/Yes related novel protein tyrosine kinase) belongs to the family of Src-related non-receptor tyrosine kinases. Consistent with physiological roles in cell growth and proliferation, aberrant function of Lyn is associated with various f ...

    Lyn kinase (Lck/Yes related novel protein tyrosine kinase) belongs to the family of Src-related non-receptor tyrosine kinases. Consistent with physiological roles in cell growth and proliferation, aberrant function of Lyn is associated with various forms of cancer, including leukemia, breast cancer and melanoma. Here, we determine a 1.3 Å resolution crystal structure of the polyproline-binding SH3 regulatory domain of human Lyn kinase, which adopts a five-stranded β-barrel fold. Mapping of cancer-associated point mutations onto this structure reveals that these amino acid substitutions are distributed throughout the SH3 domain and may affect Lyn kinase function distinctly.


    Organizational Affiliation

    Center for Structural Biology, Nashville, TN, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase LynA69Homo sapiensMutation(s): 0 
Gene Names: LYNJTK8
EC: 2.7.10.2
Find proteins for P07948 (Homo sapiens)
Explore P07948 
Go to UniProtKB:  P07948
NIH Common Fund Data Resources
PHAROS  P07948
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 61
  • Diffraction Data DOI: 10.15785/SBGRID/640 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.722α = 90
b = 46.722β = 90
c = 55.696γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM120569
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGMI122491
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesDA043680

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence