[English] 日本語
Yorodumi
- PDB-8ygx: Structure of the PYK2 from Biortus. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ygx
TitleStructure of the PYK2 from Biortus.
ComponentsProtein-tyrosine kinase 2-beta
KeywordsTRANSFERASE / Kinase / Tyrosine-protein kinase
Function / homology
Function and homology information


regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / negative regulation of bone mineralization / cortical cytoskeleton organization / activation of Janus kinase activity ...regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / negative regulation of bone mineralization / cortical cytoskeleton organization / activation of Janus kinase activity / regulation of postsynaptic density assembly / chemokine-mediated signaling pathway / apical dendrite / cellular response to fluid shear stress / regulation of release of sequestered calcium ion into cytosol / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / calcium/calmodulin-dependent protein kinase activity / sprouting angiogenesis / Interleukin-2 signaling / Signal regulatory protein family interactions / NMDA selective glutamate receptor complex / peptidyl-tyrosine autophosphorylation / positive regulation of cell-matrix adhesion / Golgi organization / positive regulation of actin filament polymerization / negative regulation of potassium ion transport / positive regulation of protein kinase activity / RHOU GTPase cycle / signaling receptor activator activity / positive regulation of excitatory postsynaptic potential / vascular endothelial growth factor receptor signaling pathway / bone resorption / cellular defense response / positive regulation of synaptic transmission, glutamatergic / postsynaptic density, intracellular component / regulation of cell adhesion / cellular response to retinoic acid / ionotropic glutamate receptor binding / positive regulation of endothelial cell migration / ionotropic glutamate receptor signaling pathway / peptidyl-tyrosine phosphorylation / tumor necrosis factor-mediated signaling pathway / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / positive regulation of neuron projection development / regulation of synaptic plasticity / VEGFA-VEGFR2 Pathway / epidermal growth factor receptor signaling pathway / long-term synaptic potentiation / neuron migration / positive regulation of angiogenesis / presynapse / regulation of cell shape / lamellipodium / protein autophosphorylation / cell body / growth cone / protein-containing complex assembly / protein tyrosine kinase activity / cell cortex / adaptive immune response / negative regulation of neuron apoptotic process / cytoskeleton / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynaptic density / positive regulation of cell migration / negative regulation of cell population proliferation / focal adhesion / neuronal cell body / positive regulation of cell population proliferation / apoptotic process / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM central domain / FERM/acyl-CoA-binding protein superfamily ...Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Zhang, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of the PYK2 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Zhang, B.
History
DepositionFeb 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein-tyrosine kinase 2-beta


Theoretical massNumber of molelcules
Total (without water)32,1901
Polymers32,1901
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.253, 94.514, 42.668
Angle α, β, γ (deg.)90.000, 91.680, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein-tyrosine kinase 2-beta / Calcium-dependent tyrosine kinase / CADTK / Calcium-regulated non-receptor proline-rich tyrosine ...Calcium-dependent tyrosine kinase / CADTK / Calcium-regulated non-receptor proline-rich tyrosine kinase / Cell adhesion kinase beta / CAK-beta / CAKB / Focal adhesion kinase 2 / FADK 2 / Proline-rich tyrosine kinase 2 / Related adhesion focal tyrosine kinase / RAFTK


Mass: 32190.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2B, FAK2, PYK2, RAFTK / Production host: Escherichia coli (E. coli)
References: UniProt: Q14289, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M MgCl2, 0.1M Bis-Tris pH5.5-5.9, 19-29% PEG3,350,1mM TCEP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→42.686 Å / Num. obs: 18990 / % possible obs: 95.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.181 / Net I/σ(I): 5.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.479 / Num. unique obs: 1444

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.686 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.875 / SU B: 5.377 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.215 / ESU R Free: 0.198
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2703 880 4.636 %
Rwork0.2067 18103 -
all0.209 --
obs-18983 95.062 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.185 Å20 Å2-0.39 Å2
2--0.141 Å20 Å2
3----0.302 Å2
Refinement stepCycle: LAST / Resolution: 2→42.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 0 204 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122120
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162039
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.8392871
X-RAY DIFFRACTIONr_angle_other_deg0.3921.7634716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.464511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37910388
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.1881093
X-RAY DIFFRACTIONr_chiral_restr0.0550.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_nbd_refined0.2110.2440
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.21862
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21046
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2162
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.28
X-RAY DIFFRACTIONr_nbd_other0.1720.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.210
X-RAY DIFFRACTIONr_mcbond_it1.4472.5541020
X-RAY DIFFRACTIONr_mcbond_other1.4472.5541020
X-RAY DIFFRACTIONr_mcangle_it2.3684.5811272
X-RAY DIFFRACTIONr_mcangle_other2.3694.5831273
X-RAY DIFFRACTIONr_scbond_it1.8242.8281100
X-RAY DIFFRACTIONr_scbond_other1.8232.831101
X-RAY DIFFRACTIONr_scangle_it3.0445.0781598
X-RAY DIFFRACTIONr_scangle_other3.0435.0791599
X-RAY DIFFRACTIONr_lrange_it5.0126.62496
X-RAY DIFFRACTIONr_lrange_other4.77225.3082433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.276880.24313530.24514810.9530.95997.29910.228
2.052-2.1080.313680.27212630.27414020.9390.93394.93580.244
2.108-2.1690.243540.21612850.21713980.9630.9795.77970.203
2.169-2.2360.247590.21412620.21613720.9560.96996.28280.202
2.236-2.3090.404640.27211520.27813020.8930.94193.39480.246
2.309-2.3890.169400.21111800.2112540.9770.97197.28870.207
2.389-2.4790.265460.19811760.20112600.9580.97596.98410.195
2.479-2.580.25510.18610450.18911380.9520.97896.30930.184
2.58-2.6950.322590.20910360.21511630.9240.9794.15310.21
2.695-2.8260.28630.2119440.21510750.940.97193.67440.217
2.826-2.9780.282510.29260.20410180.9510.97395.97250.21
2.978-3.1570.238470.2168960.2179850.970.96995.7360.224
3.157-3.3740.301370.2248470.2279220.9340.96695.87850.234
3.374-3.6420.362250.2097770.2138540.8780.9793.9110.226
3.642-3.9870.267280.1817070.1847800.9650.97694.23080.201
3.987-4.4530.228340.1666410.1697170.9650.98194.14230.191
4.453-5.1320.174240.1745660.1746370.9850.98192.62170.2
5.132-6.2630.273170.2034790.2055430.9690.97791.34440.228
6.263-8.7640.317150.2073610.2114150.9650.97590.60240.257
8.764-42.6860.202100.2072070.2072520.9620.96486.11110.235

+
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