[English] 日本語
Yorodumi
- PDB-1g83: CRYSTAL STRUCTURE OF FYN SH3-SH2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g83
TitleCRYSTAL STRUCTURE OF FYN SH3-SH2
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN
KeywordsTRANSFERASE / BETA BARREL / ANTIPARALLEL BETA SHEET / ALPHA HELIX / 3-10 HELIX
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 / regulation of glutamate receptor signaling pathway / heart process / 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 / 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 / cellular response to L-glutamate / activated T cell proliferation / positive regulation of protein localization to membrane / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / CD4 receptor binding / negative regulation of dendritic spine maintenance / feeding behavior / Co-stimulation by CD28 / Nephrin family interactions / DCC mediated attractive signaling / natural killer cell activation / EPH-Ephrin signaling / Ephrin signaling / CD28 dependent Vav1 pathway / dendritic spine maintenance / 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 / 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 / alpha-tubulin binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / postsynaptic density, intracellular component / cellular response to transforming growth factor beta stimulus / forebrain development / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / phospholipase binding / T cell receptor binding / phosphatidylinositol 3-kinase binding / GPVI-mediated activation cascade / T cell costimulation / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / 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 / Regulation of signaling by CBL / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / Cell surface interactions at the vascular wall / learning / actin filament / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / protein catabolic process / peptidyl-tyrosine phosphorylation / G protein-coupled receptor binding / Signaling by SCF-KIT / negative regulation of protein catabolic process / modulation of chemical synaptic transmission / positive regulation of neuron projection development / Signaling by CSF1 (M-CSF) in myeloid cells / tau protein binding / positive regulation of protein localization to nucleus
Similarity search - Function
: / Fyn/Yrk, SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...: / Fyn/Yrk, SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsArold, S.T. / Ulmer, T.S. / Mulhern, T.D. / Werner, J.M. / Ladbury, J.E. / Campbell, I.D. / Noble, M.E.M.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The role of the Src homology 3-Src homology 2 interface in the regulation of Src kinases.
Authors: Arold, S.T. / Ulmer, T.S. / Mulhern, T.D. / Werner, J.M. / Ladbury, J.E. / Campbell, I.D. / Noble, M.E.
History
DepositionNov 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN
B: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN


Theoretical massNumber of molelcules
Total (without water)37,8222
Polymers37,8222
Non-polymers00
Water28816
1
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN


Theoretical massNumber of molelcules
Total (without water)18,9111
Polymers18,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN


Theoretical massNumber of molelcules
Total (without water)18,9111
Polymers18,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.970, 89.960, 60.270
Angle α, β, γ (deg.)90.00, 101.44, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN / P59-FYN


Mass: 18910.930 Da / Num. of mol.: 2 / Fragment: SH3 AND SH2 DOMAIN / Mutation: C238S, C239S, C245S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06241, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6
Details: PEG 8000, sodium tartrate, TRIS , pH 6.0, VAPOR DIFFUSION, temperature 295.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris1drop
21 M1dropNaCl
316 mg/mlprotein1drop
40.25 Msodium tartrate1reservoir
512 %PEG80001reservoir
6100 mMTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9402 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9402 Å / Relative weight: 1
ReflectionResolution: 2.6→35.8 Å / Num. all: 10431 / Num. obs: 69967 / % possible obs: 82 % / Observed criterion σ(I): 0.9 / Redundancy: 2.1 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.074 / Net I/σ(I): 6.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.309 / % possible all: 83.4
Reflection
*PLUS
Num. obs: 10431 / % possible obs: 82 % / Num. measured all: 69967 / Rmerge(I) obs: 0.074

-
Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→37 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 506 -CNS
Rwork0.214 ---
all-10431 --
obs-10431 82 %-
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.6→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 0 16 2642
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.66
LS refinement shellResolution: 2.6→2.72 Å
RfactorNum. reflection% reflection
Rfree0.361 51 -
Rwork0.318 --
obs-1075 66 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 37 Å / σ(F): 0 / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35 Å2
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.361 / Rfactor Rwork: 0.318

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more