[English] 日本語
Yorodumi
- PDB-6ipy: His-tagged Fyn SH3 domain R96I mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ipy
TitleHis-tagged Fyn SH3 domain R96I mutant
ComponentsTyrosine-protein kinase Fyn
KeywordsPROTEIN BINDING / kinase / SH3 domain / hexa-histidine tag / crystal stabilized by histidine tag
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.343 Å
AuthorsArold, S.T. / Aljedani, S.S. / Shahul Hameed, U.F.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other governmentKAUST - BAS/1/1056-01 Saudi Arabia
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
DepositionNov 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author / database_2
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
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein kinase Fyn


Theoretical massNumber of molelcules
Total (without water)9,2811
Polymers9,2811
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4750 Å2
Unit cell
Length a, b, c (Å)41.520, 41.520, 32.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Tyrosine-protein kinase Fyn


Mass: 9281.111 Da / Num. of mol.: 1 / Fragment: UNP residues 82-144 / Mutation: R96I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1.52 Å3/Da / Density % sol: 18.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1M Citric acid pH 3.5 and 25%(w/v) Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.343→41.52 Å / Num. obs: 12432 / % possible obs: 98.58 % / Redundancy: 12.5 % / Biso Wilson estimate: 22.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07325 / Rpim(I) all: 0.02104 / Rrim(I) all: 0.07628 / Net I/σ(I): 20.23
Reflection shellResolution: 1.343→1.391 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.374 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 1125 / CC1/2: 0.555 / Rpim(I) all: 0.5235 / Rrim(I) all: 1.479 / % possible all: 87.67

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H0H

3h0h


Resolution: 1.343→41.52 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32
RfactorNum. reflection% reflection
Rfree0.2013 617 4.99 %
Rwork0.181 --
obs0.182 12373 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.71 Å2 / Biso mean: 39.562 Å2 / Biso min: 15.75 Å2
Refinement stepCycle: final / Resolution: 1.343→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 0 31 567
Biso mean---37.82 -
Num. residues----67
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3417-1.47680.30661440.28892786293094
1.4768-1.69050.2411560.233929543110100
1.6905-2.12980.20681560.210429733129100
2.1298-41.53990.18941610.160430433204100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.57110.9210.67631.814-1.74852.8569-0.1663-0.44960.40440.87610.229-0.1586-0.3194-0.2622-0.00650.35930.0801-0.03930.2181-0.03560.1789-3.447-10.07418.166
22.1401-0.90441.51442.799-0.94942.7772-0.1983-0.1251-0.14440.14030.23120.1181-0.2212-0.3809-0.05180.27410.0446-0.00840.2014-0.00270.2002-3.505-12.19816.445
34.18211.28752.38621.00850.99361.49390.1470.7045-0.0749-0.4633-0.3049-0.2778-0.68690.00610.03730.5179-0.01780.06840.57210.02720.66814.651-9.1279.298
42.4221-0.36910.87284.9792-1.42063.434-0.114-0.2153-0.07580.10.27230.2708-0.0344-0.3465-0.13580.19180.0345-0.01930.19540.00040.1763-3.064-16.84617.174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 105:118 )A105 - 118
2X-RAY DIFFRACTION2( CHAIN A AND RESID 119:143 )A119 - 143
3X-RAY DIFFRACTION3( CHAIN A AND RESID 144:148 )A144 - 148
4X-RAY DIFFRACTION4( CHAIN A AND RESID 82:104 )A82 - 104

+
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