[English] 日本語
Yorodumi
- PDB-3a4o: Lyn kinase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3a4o
TitleLyn kinase domain
ComponentsTyrosine-protein kinase Lyn
KeywordsTRANSFERASE / Src family / kinase domain / Alternative splicing / ATP-binding / Host-virus interaction / Kinase / Lipoprotein / Myristate / Nucleotide-binding / Palmitate / Phosphoprotein / Polymorphism / Proto-oncogene / Tyrosine-protein kinase
Function / homology
Function and homology information


negative regulation of myeloid leukocyte differentiation / C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / response to sterol depletion / regulation of mast cell activation / eosinophil differentiation / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / negative regulation of intracellular signal transduction / Fc receptor mediated inhibitory signaling pathway ...negative regulation of myeloid leukocyte differentiation / C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / response to sterol depletion / regulation of mast cell activation / eosinophil differentiation / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / negative regulation of intracellular signal transduction / Fc receptor mediated inhibitory signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / regulation of B cell receptor signaling pathway / negative regulation of toll-like receptor 2 signaling pathway / positive regulation of oligodendrocyte progenitor proliferation / tolerance induction to self antigen / integrin alpha2-beta1 complex / negative regulation of mast cell proliferation / positive regulation of mast cell proliferation / immune response-regulating cell surface receptor signaling pathway / glycosphingolipid binding / platelet degranulation / regulation of mast cell degranulation / negative regulation of toll-like receptor 4 signaling pathway / positive regulation of amyloid precursor protein catabolic process / negative regulation of immune response / regulation of platelet aggregation / phosphorylation-dependent protein binding / dendritic cell differentiation / regulation of B cell apoptotic process / neuroinflammatory response / phosphatidylinositol 3-kinase activator activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / interleukin-5-mediated signaling pathway / Erythropoietin activates Phospholipase C gamma (PLCG) / Platelet Adhesion to exposed collagen / histamine secretion by mast cell / CD22 mediated BCR regulation / regulation of release of sequestered calcium ion into cytosol / oligodendrocyte development / response to carbohydrate / gamma-tubulin binding / platelet-derived growth factor receptor binding / Co-stimulation by CD28 / regulation of protein phosphorylation / Fc epsilon receptor (FCERI) signaling / EPH-Ephrin signaling / postsynaptic specialization, intracellular component / Regulation of KIT signaling / toll-like receptor 4 signaling pathway / leukocyte migration / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / negative regulation of B cell proliferation / Dectin-2 family / mitochondrial crista / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / regulation of cell adhesion mediated by integrin / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of protein phosphorylation / PECAM1 interactions / negative regulation of MAP kinase activity / B cell homeostasis / signaling receptor activator activity / FCGR activation / EPH-ephrin mediated repulsion of cells / positive regulation of phosphorylation / growth hormone receptor signaling pathway via JAK-STAT / Role of LAT2/NTAL/LAB on calcium mobilization / response to amino acid / ephrin receptor signaling pathway / response to axon injury / fatty acid transport / regulation of ERK1 and ERK2 cascade / hematopoietic progenitor cell differentiation / Growth hormone receptor signaling / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / GPVI-mediated activation cascade / response to hormone / T cell costimulation / cellular response to retinoic acid / ephrin receptor binding / positive regulation of glial cell proliferation / EPHB-mediated forward signaling / FCERI mediated Ca+2 mobilization / CD209 (DC-SIGN) signaling / regulation of cytokine production / FCGR3A-mediated IL10 synthesis / Regulation of signaling by CBL / 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 / lipopolysaccharide-mediated signaling pathway / DNA damage checkpoint signaling / erythrocyte differentiation / Cell surface interactions at the vascular wall / B cell receptor signaling pathway
Similarity search - Function
Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / : / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
STAUROSPORINE / Tyrosine-protein kinase Lyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMiyano, N. / Kinoshita, T. / Tada, T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Structural basis for the inhibitor recognition of human Lyn kinase domain
Authors: Miyano, N. / Kinoshita, T. / Nakai, R. / Kirii, Y. / Yokota, K. / Tada, T.
History
DepositionJul 11, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Tyrosine-protein kinase Lyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4612
Polymers32,9951
Non-polymers4671
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.382, 128.382, 54.875
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Tyrosine-protein kinase Lyn


Mass: 32994.816 Da / Num. of mol.: 1 / Fragment: residues in UNP 233-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P07948, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 6212 / Num. obs: 5892
Reflection shellResolution: 3→3.14 Å

-
Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DQ7

2dq7


Resolution: 3→50 Å / σ(F): 0
RfactorNum. reflection
Rfree0.324 -
Rwork0.293 -
all-6212
obs-5892
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 35 0 2112
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg2.1

+
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