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- PDB-3h0h: human Fyn SH3 domain R96I mutant, crystal form I -

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Basic information

Entry
Database: PDB / ID: 3h0h
Titlehuman Fyn SH3 domain R96I mutant, crystal form I
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 / regulation of glutamate receptor signaling pathway / heart process / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / regulation of glutamate receptor signaling pathway / heart process / 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 / CRMPs in Sema3A signaling / G protein-coupled glutamate receptor signaling pathway / FLT3 signaling through SRC family kinases / activated T cell proliferation / positive regulation of protein localization to membrane / type 5 metabotropic glutamate receptor binding / CD4 receptor binding / Nef and signal transduction / cellular response to L-glutamate / feeding behavior / Co-stimulation by CD28 / Nephrin family interactions / DCC mediated attractive signaling / EPH-Ephrin signaling / natural killer cell activation / negative regulation of dendritic spine maintenance / Ephrin signaling / CD28 dependent Vav1 pathway / dendritic spine maintenance / growth factor receptor binding / cellular response to peptide hormone stimulus / tau-protein kinase activity / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / dendrite morphogenesis / peptide hormone receptor binding / CD8 receptor binding / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / PECAM1 interactions / response to amyloid-beta / cellular response to glycine / FCGR activation / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / glial cell projection / CD28 dependent PI3K/Akt signaling / positive regulation of protein targeting to membrane / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ephrin receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / alpha-tubulin binding / cellular response to transforming growth factor beta stimulus / postsynaptic density, intracellular component / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / T cell receptor binding / phosphatidylinositol 3-kinase binding / phospholipase binding / GPVI-mediated activation cascade / ephrin receptor binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / negative regulation of protein ubiquitination / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / peptidyl-tyrosine phosphorylation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / Cell surface interactions at the vascular wall / learning / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / actin filament / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / protein catabolic process / Signaling by SCF-KIT / G protein-coupled receptor binding / positive regulation of neuron projection development / negative regulation of protein catabolic process / modulation of chemical synaptic transmission / positive regulation of protein localization to nucleus / VEGFA-VEGFR2 Pathway / tau protein 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 / SH3 type barrels. ...: / Fyn/Yrk, SH3 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 Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDumas, C. / Strub, M.-P. / 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: Advisory / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,2242
Polymers8,0301
Non-polymers1941
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.907, 41.907, 32.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 8029.742 Da / Num. of mol.: 1 / Fragment: SH3 domain, UNP residues 73-142 / Mutation: R96I
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 1.7914 Å3/Da / Density % sol: 31.3405 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5M ammonium sulphate, 0.1M sodium citrate, 1.0M lithium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 20, 2004 / Details: osmic mirror
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.76→20.95 Å / Num. obs: 5700 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.04 / Net I/σ(I): 25.2
Reflection shellResolution: 1.76→1.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 12.3 / Num. unique all: 1798 / Rsym value: 0.064 / % possible all: 92.7

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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: 1.76→20.95 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.907 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.126 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22191 459 8.1 %RANDOM
Rwork0.16567 ---
all0.17012 5235 --
obs0.17012 5235 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.747 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.76→20.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms494 0 13 35 542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022519
X-RAY DIFFRACTIONr_bond_other_d0.0030.0218
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.956703
X-RAY DIFFRACTIONr_angle_other_deg1.164342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.728562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85425.225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6321573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg36.266151
X-RAY DIFFRACTIONr_chiral_restr0.2490.274
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021400
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_it2.9834310
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.4816497
X-RAY DIFFRACTIONr_scbond_it3.7884209
X-RAY DIFFRACTIONr_scangle_it5.716206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.757→1.803 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 30 -
Rwork0.211 348 -
obs--87.91 %
Refinement TLS params.Method: refined / Origin x: 27.9478 Å / Origin y: 3.557 Å / Origin z: -0.0954 Å
111213212223313233
T0.0067 Å2-0.0058 Å2-0.0023 Å2-0.0276 Å20.0135 Å2--0.0101 Å2
L1.6233 °20.6582 °2-0.5347 °2-1.4523 °2-0.6264 °2--1.131 °2
S0.0674 Å °-0.0159 Å °-0.0105 Å °0.0611 Å °-0.0942 Å °-0.048 Å °-0.0643 Å °0.0055 Å °0.0267 Å °

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