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- PDB-6nmw: Crystal structure of the human Lyn SH3 domain -

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Basic information

Entry
Database: PDB / ID: 6nmw
TitleCrystal structure of the human Lyn SH3 domain
ComponentsTyrosine-protein kinase Lyn
KeywordsONCOPROTEIN / LYN kinase / Src family kinase / non-receptor tyrosine kinase / SH3 domain
Function / homology
Function and homology information


C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / negative regulation of intracellular signal transduction / response to sterol depletion / regulation of mast cell activation / negative regulation of myeloid leukocyte differentiation / eosinophil differentiation / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / positive regulation of oligodendrocyte progenitor proliferation ...C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / negative regulation of intracellular signal transduction / response to sterol depletion / regulation of mast cell activation / negative regulation of myeloid leukocyte differentiation / eosinophil differentiation / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / positive regulation of oligodendrocyte progenitor proliferation / positive regulation of Fc receptor mediated stimulatory signaling pathway / Fc receptor mediated inhibitory signaling pathway / regulation of B cell receptor signaling pathway / tolerance induction to self antigen / negative regulation of toll-like receptor 2 signaling pathway / integrin alpha2-beta1 complex / immune response-regulating cell surface receptor signaling pathway / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of mast cell proliferation / negative regulation of mast cell proliferation / glycosphingolipid binding / platelet degranulation / negative regulation of toll-like receptor 4 signaling pathway / regulation of mast cell degranulation / phosphorylation-dependent protein binding / regulation of platelet aggregation / dendritic cell differentiation / regulation of B cell apoptotic process / phosphatidylinositol 3-kinase activator activity / oligodendrocyte development / Signaling by Erythropoietin / response to carbohydrate / Erythropoietin activates STAT5 / interleukin-5-mediated signaling pathway / Erythropoietin activates Phospholipase C gamma (PLCG) / CD28 co-stimulation / Platelet Adhesion to exposed collagen / negative regulation of immune response / histamine secretion by mast cell / regulation of release of sequestered calcium ion into cytosol / CD22 mediated BCR regulation / platelet-derived growth factor receptor binding / gamma-tubulin binding / EPH-Ephrin signaling / Fc epsilon receptor (FCERI) signaling / toll-like receptor 4 signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / Regulation of KIT signaling / postsynaptic specialization, intracellular component / leukocyte migration / CTLA4 inhibitory signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / EPHA-mediated growth cone collapse / Dectin-2 family / negative regulation of B cell proliferation / B cell homeostasis / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / mitochondrial crista / PECAM1 interactions / regulation of cell adhesion mediated by integrin / FCGR activation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / response to axon injury / response to amino acid / growth hormone receptor signaling pathway via JAK-STAT / Role of LAT2/NTAL/LAB on calcium mobilization / hematopoietic progenitor cell differentiation / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / fatty acid transport / Growth hormone receptor signaling / cell surface receptor protein tyrosine kinase signaling pathway / lipopolysaccharide-mediated signaling pathway / cellular response to retinoic acid / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of MAP kinase activity / positive regulation of glial cell proliferation / GPVI-mediated activation cascade / T cell costimulation / regulation of cytokine production / EPHB-mediated forward signaling / ephrin receptor binding / CD209 (DC-SIGN) signaling / regulation of ERK1 and ERK2 cascade / response to hormone / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / negative regulation of protein phosphorylation / erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / DNA damage checkpoint signaling / Regulation of signaling by CBL / negative regulation of inflammatory response to antigenic stimulus / Cell surface interactions at the vascular wall / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / adherens junction
Similarity search - Function
Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. ...Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Lyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 Å
AuthorsBerndt, S. / Gurevich, V.V. / Iverson, T.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120569 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GMI122491 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DA043680 United States
CitationJournal: PLoS ONE / Year: 2019
Title: Crystal structure of the SH3 domain of human Lyn non-receptor tyrosine kinase.
Authors: Berndt, S. / Gurevich, V.V. / Iverson, T.M.
History
DepositionJan 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Lyn


Theoretical massNumber of molelcules
Total (without water)8,0751
Polymers8,0751
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4260 Å2
Unit cell
Length a, b, c (Å)46.722, 46.722, 55.696
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Tyrosine-protein kinase Lyn / Lck/Yes-related novel protein tyrosine kinase / V-yes-1 Yamaguchi sarcoma viral related oncogene ...Lck/Yes-related novel protein tyrosine kinase / V-yes-1 Yamaguchi sarcoma viral related oncogene homolog / p53Lyn / p56Lyn


Mass: 8075.152 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYN, JTK8 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07948, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na citrate, 3.2 M NaCl

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.199→50 Å / Num. obs: 18850 / % possible obs: 87.09 % / Redundancy: 5.7 % / CC1/2: 0.994 / Rpim(I) all: 0.012 / Rsym value: 0.038 / Net I/σ(I): 3.55
Reflection shellResolution: 1.2→1.22 Å / Num. unique obs: 12664 / CC1/2: 0.923 / Rpim(I) all: 0.171 / Rsym value: 0.512 / % possible all: 81.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IIM

2iim


Resolution: 1.199→32.736 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.77
RfactorNum. reflection% reflection
Rfree0.1827 925 4.91 %
Rwork0.1725 --
obs0.173 18850 87.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.199→32.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms511 0 0 40 551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014554
X-RAY DIFFRACTIONf_angle_d1.602749
X-RAY DIFFRACTIONf_dihedral_angle_d15.618213
X-RAY DIFFRACTIONf_chiral_restr0.10977
X-RAY DIFFRACTIONf_plane_restr0.01695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1993-1.26260.2551840.21377X-RAY DIFFRACTION47
1.2626-1.34170.21261330.17362696X-RAY DIFFRACTION92
1.3417-1.44530.15441100.16222698X-RAY DIFFRACTION92
1.4453-1.59070.19131320.16392783X-RAY DIFFRACTION95
1.5907-1.82090.16641410.16142754X-RAY DIFFRACTION93
1.8209-2.2940.18321610.16062773X-RAY DIFFRACTION95
2.294-32.74780.18231640.18252844X-RAY DIFFRACTION96

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