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- PDB-3h0f: Crystal structure of the human Fyn SH3 R96W mutant -

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Basic information

Entry
Database: PDB / ID: 3h0f
TitleCrystal structure of the human Fyn SH3 R96W mutant
ComponentsProto-oncogene tyrosine-protein kinase Fyn
KeywordsTRANSFERASE / beta barrel
Function / homology
Function and homology information


negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / heart process / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / heart process / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / reelin-mediated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of protein localization to membrane / cellular response to L-glutamate / G protein-coupled glutamate receptor signaling pathway / CRMPs in Sema3A signaling / activated T cell proliferation / FLT3 signaling through SRC family kinases / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / negative regulation of dendritic spine maintenance / feeding behavior / Co-stimulation by CD28 / Nephrin family interactions / natural killer cell activation / DCC mediated attractive signaling / EPH-Ephrin signaling / Ephrin signaling / dendritic spine maintenance / CD28 dependent Vav1 pathway / dendrite morphogenesis / tau-protein kinase activity / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / PECAM1 interactions / response to amyloid-beta / cellular response to glycine / FCGR activation / Sema3A PAK dependent Axon repulsion / glial cell projection / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / CD28 dependent PI3K/Akt signaling / Role of LAT2/NTAL/LAB on calcium mobilization / alpha-tubulin binding / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / forebrain development / cellular response to transforming growth factor beta stimulus / GPVI-mediated activation cascade / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / T cell costimulation / Signaling by ERBB2 / EPHB-mediated forward signaling / negative regulation of protein ubiquitination / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / learning / Cell surface interactions at the vascular wall / actin filament / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / G protein-coupled receptor binding / modulation of chemical synaptic transmission / protein catabolic process / Signaling by SCF-KIT / Schaffer collateral - CA1 synapse / peptidyl-tyrosine phosphorylation / negative regulation of protein catabolic process / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / tau protein binding / VEGFA-VEGFR2 Pathway / cellular response to hydrogen peroxide / cellular response to amyloid-beta / neuron migration / Signaling by CSF1 (M-CSF) in myeloid cells / calcium ion transport / Constitutive Signaling by Aberrant PI3K in Cancer / disordered domain specific binding
Similarity search - Function
: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily ...: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / 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
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsPonchon, L. / Hoh, F. / Labesse, G. / Dumas, C. / Arold, S.T.
CitationJournal: Biochem.J. / Year: 2021
Title: Synergy and allostery in ligand binding by HIV-1 Nef.
Authors: Aldehaiman, A. / Momin, A.A. / Restouin, A. / Wang, L. / Shi, X. / Aljedani, S. / Opi, S. / Lugari, A. / Shahul Hameed, U.F. / Ponchon, L. / Morelli, X. / Huang, M. / Dumas, C. / Collette, Y. / Arold, S.T.
History
DepositionApr 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 10, 2021Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2812
Polymers8,1031
Non-polymers1781
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.103, 52.103, 53.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Fyn / Fyn tyrosine kinase / p59-Fyn / Protooncogene Syn / SLK


Mass: 8102.793 Da / Num. of mol.: 1 / Fragment: SH3 domain, UNP residues 73-142 / Mutation: R96W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 2.0M ammonium sulphate, 2% PEG 400, 0.1M Tris, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 27, 2004 / Details: osmic mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.61→30.3 Å / Num. all: 2270 / Num. obs: 2270 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.13 / Net I/σ(I): 13.4
Reflection shellResolution: 2.61→2.72 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.7 / Num. unique all: 542 / Rsym value: 0.52 / % possible all: 58.2

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1shf

1shf


Resolution: 2.61→30.3 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.863 / SU B: 10.739 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.18 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28226 216 9.3 %RANDOM
Rwork0.20199 ---
all0.20912 2119 --
obs0.20912 2119 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.61→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms481 0 12 9 502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022507
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.939689
X-RAY DIFFRACTIONr_angle_other_deg0.156342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.375558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5642526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3441571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.459151
X-RAY DIFFRACTIONr_chiral_restr0.1160.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021394
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1181.5293
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1512472
X-RAY DIFFRACTIONr_scbond_it2.6153214
X-RAY DIFFRACTIONr_scangle_it4.6494.5217
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.612→2.679 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 18 -
Rwork0.264 109 -
obs--73.84 %

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