6NMW

Crystal structure of the human Lyn SH3 domain

• PDB DOI: https://doi.org/10.2210/pdb6NMW/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-12 Released: 2019-04-17 
• Deposition Author(s): Berndt, S., Gurevich, V.V., Iverson, T.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

---

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 

Starting Model: experimental

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

• PubMed: 30969999 
• DOI: https://doi.org/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 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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Lyn	A	69	Homo sapiens	Mutation(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

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: https://doi.org/10.15785/SBGRID/640

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.722	α = 90
b = 46.722	β = 90
c = 55.696	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): Berndt, S., Gurevich, V.V., Iverson, T.M.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM120569
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GMI122491
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	DA043680

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