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- PDB-4tzi: Structure of unliganded Lyn SH2 domain -

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Basic information

Entry
Database: PDB / ID: 4tzi
TitleStructure of unliganded Lyn SH2 domain
ComponentsTyrosine-protein kinase Lyn
KeywordsTRANSFERASE / SH2 domain
Function / homology
Function and homology information


Platelet Adhesion to exposed collagen / Dectin-2 family / Signaling by Erythropoietin / Growth hormone receptor signaling / erythropoietin receptor binding / C-X-C chemokine receptor CXCR4 signaling pathway / negative regulation of intracellular signal transduction / Fc receptor mediated stimulatory signaling pathway / response to sterol depletion / regulation of mast cell activation ...Platelet Adhesion to exposed collagen / Dectin-2 family / Signaling by Erythropoietin / Growth hormone receptor signaling / erythropoietin receptor binding / C-X-C chemokine receptor CXCR4 signaling pathway / negative regulation of intracellular signal transduction / Fc receptor mediated stimulatory signaling pathway / response to sterol depletion / regulation of mast cell activation / positive regulation of stress-activated protein kinase signaling cascade / Fc epsilon receptor (FCERI) signaling / regulation of monocyte chemotaxis / PECAM1 interactions / CD22 mediated BCR regulation / CD28 co-stimulation / Signaling by CSF3 (G-CSF) / negative regulation of myeloid leukocyte differentiation / CTLA4 inhibitory signaling / Erythropoietin activates RAS / eosinophil differentiation / Regulation of KIT signaling / Role of LAT2/NTAL/LAB on calcium mobilization / EPHA-mediated growth cone collapse / positive regulation of Fc receptor mediated stimulatory signaling pathway / tolerance induction to self antigen / positive regulation of dendritic cell apoptotic process / positive regulation of oligodendrocyte progenitor proliferation / GPVI-mediated activation cascade / Fc receptor mediated inhibitory signaling pathway / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / regulation of B cell receptor signaling pathway / FCERI mediated MAPK activation / Inactivation of CSF3 (G-CSF) signaling / integrin alpha2-beta1 complex / negative regulation of toll-like receptor 2 signaling pathway / immune response-regulating cell surface receptor signaling pathway / Signaling by SCF-KIT / FCGR activation / Cyclin D associated events in G1 / positive regulation of mast cell proliferation / negative regulation of mast cell proliferation / glycosphingolipid binding / FCERI mediated Ca+2 mobilization / phosphorylation-dependent protein binding / hemoglobin biosynthetic process / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / negative regulation of toll-like receptor 4 signaling pathway / FCERI mediated NF-kB activation / platelet degranulation / regulation of mast cell degranulation / Cell surface interactions at the vascular wall / dendritic cell differentiation / Regulation of signaling by CBL / : / regulation of platelet aggregation / regulation of B cell apoptotic process / oligodendrocyte development / CD209 (DC-SIGN) signaling / histamine secretion by mast cell / phosphatidylinositol 3-kinase activator activity / interleukin-5-mediated signaling pathway / regulation of release of sequestered calcium ion into cytosol / gamma-tubulin binding / response to carbohydrate / platelet-derived growth factor receptor binding / toll-like receptor 4 signaling pathway / postsynaptic specialization, intracellular component / negative regulation of B cell proliferation / mitochondrial crista / regulation of cell adhesion mediated by integrin / B cell homeostasis / hemopoiesis / response to axon injury / response to amino acid / hematopoietic progenitor cell differentiation / cellular response to retinoic acid / positive regulation of glial cell proliferation / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / regulation of cytokine production / lipopolysaccharide-mediated signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / ephrin receptor binding / response to hormone / erythrocyte differentiation / regulation of ERK1 and ERK2 cascade / negative regulation of MAP kinase activity / negative regulation of protein phosphorylation / mitochondrial membrane / phosphoprotein binding / adherens junction / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / response to insulin / non-membrane spanning protein tyrosine kinase activity / regulation of erythrocyte differentiation / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade
Similarity search - Function
Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains ...Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Lyn
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWybenga-Groot, L.E.
CitationJournal: Mol.Cell Proteomics / Year: 2015
Title: Tyrosine Phosphorylation of the Lyn Src Homology 2 (SH2) Domain Modulates Its Binding Affinity and Specificity.
Authors: Jin, L.L. / Wybenga-Groot, L.E. / Tong, J. / Taylor, P. / Minden, M.D. / Trudel, S. / McGlade, C.J. / Moran, M.F.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Lyn
B: Tyrosine-protein kinase Lyn


Theoretical massNumber of molelcules
Total (without water)26,3982
Polymers26,3982
Non-polymers00
Water1,892105
1
A: Tyrosine-protein kinase Lyn


Theoretical massNumber of molelcules
Total (without water)13,1991
Polymers13,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase Lyn


Theoretical massNumber of molelcules
Total (without water)13,1991
Polymers13,1991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.915, 27.995, 74.915
Angle α, β, γ (deg.)90.000, 96.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13199.002 Da / Num. of mol.: 2 / Fragment: SH2 domain residues 115-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lyn / Production host: Escherichia coli (E. coli)
References: UniProt: P25911, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 ul seed stock with 0.2 ul well solution (0.1 M Tris pH 8.5, 20% v/v ethanol) and 0.3 ul of protein (20 mM Hepes pH 7.0, 150 mM NaCl, 1 mM DTT, 22.5 mg/mL)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 21, 2012
RadiationMonochromator: Varimax VHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 13934 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 26.53 Å2 / Net I/σ(I): 25.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 10.2 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data collection
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HCK

3hck


Resolution: 2.1→32.756 Å / FOM work R set: 0.7963 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 1062 7.63 %Random
Rwork0.199 12857 --
obs0.2033 13919 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.64 Å2 / Biso mean: 40.86 Å2 / Biso min: 14.21 Å2
Refinement stepCycle: final / Resolution: 2.1→32.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 0 105 1819
Biso mean---39.64 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091749
X-RAY DIFFRACTIONf_angle_d1.0932355
X-RAY DIFFRACTIONf_chiral_restr0.044254
X-RAY DIFFRACTIONf_plane_restr0.005303
X-RAY DIFFRACTIONf_dihedral_angle_d12.882647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.19580.26771150.211216221737
2.1958-2.31150.25541440.228115771721
2.3115-2.45630.30231530.225915361689
2.4563-2.64590.30171130.222716031716
2.6459-2.9120.27121300.222315991729
2.912-3.3330.28781340.212916111745
3.333-4.19790.22611270.176616271754
4.1979-32.76030.22481460.177816821828
Refinement TLS params.Method: refined / Origin x: 27.2063 Å / Origin y: 32.3366 Å / Origin z: 19.0802 Å
111213212223313233
T0.2191 Å2-0.0718 Å2-0.0309 Å2-0.1984 Å2-0.0001 Å2--0.1892 Å2
L0.4052 °2-0.2001 °2-0.444 °2-0.8408 °2-1.39 °2--2.1605 °2
S0.0171 Å °0.0868 Å °-0.0091 Å °-0.0334 Å °-0.0897 Å °-0.0198 Å °-0.032 Å °0.1838 Å °0.0059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA119 - 228
2X-RAY DIFFRACTION1allB120 - 228
3X-RAY DIFFRACTION1allS1 - 113

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