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- PDB-4eik: Crystal Structure of the Human Fyn SH3 domain in complex with the... -

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Basic information

Entry
Database: PDB / ID: 4eik
TitleCrystal Structure of the Human Fyn SH3 domain in complex with the synthetic peptide VSL12
Components
  • Tyrosine-protein kinase Fyn
  • VSL12 peptide
KeywordsTRANSFERASE/PROTEIN BINDING / beta barrel / proline rich motifs / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / Platelet Adhesion to exposed collagen / G protein-coupled glutamate receptor signaling pathway / CD28 co-stimulation / positive regulation of protein localization to membrane / activated T cell proliferation / CRMPs in Sema3A signaling / positive regulation of cysteine-type endopeptidase activity / FLT3 signaling through SRC family kinases / feeding behavior / Nef and signal transduction / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / Nephrin family interactions / DCC mediated attractive signaling / dendrite morphogenesis / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / tau-protein kinase activity / CTLA4 inhibitory signaling / phospholipase activator activity / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / glial cell projection / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / Sema3A PAK dependent Axon repulsion / cellular response to glycine / alpha-tubulin binding / FCGR activation / EPH-ephrin mediated repulsion of cells / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / 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 / regulation of peptidyl-tyrosine phosphorylation / forebrain development / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / Signaling by ERBB2 / negative regulation of protein ubiquitination / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / EPHB-mediated forward signaling / T cell costimulation / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / ephrin receptor binding / FCGR3A-mediated IL10 synthesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / learning / actin filament / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / cell surface receptor protein tyrosine kinase signaling pathway / axon guidance / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / protein catabolic process / modulation of chemical synaptic transmission / tau protein binding / Signaling by SCF-KIT / negative regulation of protein catabolic process / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / cellular response to hydrogen peroxide / positive regulation of protein localization to nucleus / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / Constitutive Signaling by Aberrant PI3K in Cancer / calcium ion transport / Signaling by CSF1 (M-CSF) in myeloid cells / 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 / SH3 type barrels. / Src homology 3 domains ...: / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsCamara-Artigas, A.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystallization of and selenomethionine phasing strategy for a SETMAR-DNA complex.
Authors: Chen, Q. / Georgiadis, M.
History
DepositionApr 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Fyn
B: VSL12 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5123
Polymers8,4892
Non-polymers231
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-14 kcal/mol
Surface area4260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.843, 81.843, 35.904
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Tyrosine-protein kinase Fyn / Proto-oncogene Syn / Proto-oncogene c-Fyn / Src-like kinase / SLK / p59-Fyn


Mass: 7171.764 Da / Num. of mol.: 1 / Fragment: SH3 domain (UNP residues 81-143)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Protein/peptide VSL12 peptide


Mass: 1317.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / 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: 4.09 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5.5 M sodium formate, 0.1 M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2009
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→19.658 Å / Num. all: 18343 / Num. obs: 17446 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 19.13 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 71.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 10 / Rsym value: 0.23 / % possible all: 72.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.85 Å19.74 Å
Translation1.85 Å19.74 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UA7

3ua7


Resolution: 1.6→19.658 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.2061 / WRfactor Rwork: 0.1842 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.879 / SU B: 0.992 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0594 / SU Rfree: 0.0616 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 885 5.1 %RANDOM
Rwork0.1742 ---
obs0.1752 17446 95.05 %-
all-18343 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.19 Å2 / Biso mean: 24.4881 Å2 / Biso min: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.18 Å2-0 Å2
2--0.37 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms555 0 1 40 596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02578
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.974791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.796569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47723.57128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5231587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.246154
X-RAY DIFFRACTIONr_chiral_restr0.1640.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022455
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 43 -
Rwork0.245 884 -
all-927 -
obs--69.13 %

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