6NMW | pdb_00006nmw

Crystal structure of the human Lyn SH3 domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.183 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 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: https://doi.org/10.1371/journal.pone.0215140
  • Primary Citation 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 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: 
    • Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America.

Macromolecule Content 

  • Total Structure Weight: 8.08 kDa 
  • Atom Count: 578 
  • Modeled Residue Count: 63 
  • Deposited Residue Count: 69 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase Lyn69Homo sapiensMutation(s): 0 
Gene Names: LYN, JTK8
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P07948 (Homo sapiens)
Explore P07948 
Go to UniProtKB:  P07948
PHAROS:  P07948
GTEx:  ENSG00000254087 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07948
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.183 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 61
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

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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  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description