[English] 日本語
Yorodumi
- PDB-6nmw: Crystal structure of the human Lyn SH3 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nmw
TitleCrystal structure of the human Lyn SH3 domain
ComponentsTyrosine-protein kinase Lyn
KeywordsONCOPROTEIN / LYN kinase / Src family kinase / non-receptor tyrosine kinase / SH3 domain
Function / homology
Function and homology information


C-X-C chemokine receptor CXCR4 signaling pathway / response to sterol depletion / positive regulation of mast cell proliferation / regulation of monocyte chemotaxis / negative regulation of myeloid leukocyte differentiation / regulation of mast cell activation / eosinophil differentiation / negative regulation of mast cell proliferation / tolerance induction to self antigen / positive regulation of dendritic cell apoptotic process ...C-X-C chemokine receptor CXCR4 signaling pathway / response to sterol depletion / positive regulation of mast cell proliferation / regulation of monocyte chemotaxis / negative regulation of myeloid leukocyte differentiation / regulation of mast cell activation / eosinophil differentiation / negative regulation of mast cell proliferation / tolerance induction to self antigen / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / Fc receptor mediated inhibitory signaling pathway / negative regulation of intracellular signal transduction / regulation of B cell receptor signaling pathway / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of B cell receptor signaling pathway / positive regulation of oligodendrocyte progenitor proliferation / integrin alpha2-beta1 complex / glycosphingolipid binding / immune response-regulating cell surface receptor signaling pathway / Assembly and Release of Dengue Virus Virions / regulation of mast cell degranulation / platelet degranulation / negative regulation of toll-like receptor 4 signaling pathway / positive regulation of amyloid precursor protein catabolic process / regulation of platelet aggregation / negative regulation of immune response / negative regulation of B cell proliferation / B cell homeostasis / positive regulation of toll-like receptor 4 signaling pathway / dendritic cell differentiation / phosphorylation-dependent protein binding / regulation of B cell apoptotic process / Signaling by Erythropoietin / phosphatidylinositol 3-kinase activator activity / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Platelet Adhesion to exposed collagen / response to carbohydrate / CD22 mediated BCR regulation / histamine secretion by mast cell / oligodendrocyte development / positive regulation of glial cell proliferation / regulation of release of sequestered calcium ion into cytosol / interleukin-5-mediated signaling pathway / regulation of cell adhesion mediated by integrin / gamma-tubulin binding / platelet-derived growth factor receptor binding / Fc epsilon receptor (FCERI) signaling / Co-stimulation by CD28 / EPH-Ephrin signaling / B cell proliferation / postsynaptic specialization, intracellular component / toll-like receptor 4 signaling pathway / leukocyte migration / Regulation of KIT signaling / regulation of erythrocyte differentiation / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / negative regulation of MAP kinase activity / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / mitochondrial crista / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway / PECAM1 interactions / hematopoietic progenitor cell differentiation / negative regulation of protein phosphorylation / lipopolysaccharide-mediated signaling pathway / FCGR activation / response to amino acid / signaling receptor activator activity / response to axon injury / regulation of protein phosphorylation / growth hormone receptor signaling pathway via JAK-STAT / positive regulation of phosphorylation / EPH-ephrin mediated repulsion of cells / Role of LAT2/NTAL/LAB on calcium mobilization / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / fatty acid transport / Growth hormone receptor signaling / T cell costimulation / cellular response to retinoic acid / ephrin receptor binding / GPVI-mediated activation cascade / DNA damage checkpoint signaling / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / EPHB-mediated forward signaling / response to hormone / peptidyl-tyrosine phosphorylation / FCERI mediated Ca+2 mobilization / regulation of cytokine production / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / erythrocyte differentiation
Similarity search - Function
Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / Src homology 2 domains / SH2 domain ...Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / 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 / 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 Lyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 Å
AuthorsBerndt, S. / Gurevich, V.V. / Iverson, T.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120569 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GMI122491 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DA043680 United States
CitationJournal: PLoS ONE / Year: 2019
Title: Crystal structure of the SH3 domain of human Lyn non-receptor tyrosine kinase.
Authors: Berndt, S. / Gurevich, V.V. / Iverson, T.M.
History
DepositionJan 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein kinase Lyn


Theoretical massNumber of molelcules
Total (without water)8,0751
Polymers8,0751
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4260 Å2
Unit cell
Length a, b, c (Å)46.722, 46.722, 55.696
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Tyrosine-protein kinase Lyn / Lck/Yes-related novel protein tyrosine kinase / V-yes-1 Yamaguchi sarcoma viral related oncogene ...Lck/Yes-related novel protein tyrosine kinase / V-yes-1 Yamaguchi sarcoma viral related oncogene homolog / p53Lyn / p56Lyn


Mass: 8075.152 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYN, JTK8 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07948, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na citrate, 3.2 M NaCl

-
Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.199→50 Å / Num. obs: 18850 / % possible obs: 87.09 % / Redundancy: 5.7 % / CC1/2: 0.994 / Rpim(I) all: 0.012 / Rsym value: 0.038 / Net I/σ(I): 3.55
Reflection shellResolution: 1.2→1.22 Å / Num. unique obs: 12664 / CC1/2: 0.923 / Rpim(I) all: 0.171 / Rsym value: 0.512 / % possible all: 81.8

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IIM

2iim


Resolution: 1.199→32.736 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.77
RfactorNum. reflection% reflection
Rfree0.1827 925 4.91 %
Rwork0.1725 --
obs0.173 18850 87.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.199→32.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms511 0 0 40 551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014554
X-RAY DIFFRACTIONf_angle_d1.602749
X-RAY DIFFRACTIONf_dihedral_angle_d15.618213
X-RAY DIFFRACTIONf_chiral_restr0.10977
X-RAY DIFFRACTIONf_plane_restr0.01695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1993-1.26260.2551840.21377X-RAY DIFFRACTION47
1.2626-1.34170.21261330.17362696X-RAY DIFFRACTION92
1.3417-1.44530.15441100.16222698X-RAY DIFFRACTION92
1.4453-1.59070.19131320.16392783X-RAY DIFFRACTION95
1.5907-1.82090.16641410.16142754X-RAY DIFFRACTION93
1.8209-2.2940.18321610.16062773X-RAY DIFFRACTION95
2.294-32.74780.18231640.18252844X-RAY DIFFRACTION96

+
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