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- PDB-3gm1: Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of... -

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Basic information

Entry
Database: PDB / ID: 3gm1
TitleCrystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 in Complex with Paxillin LD4 Motif-Derived Peptides
Components
  • Paxillin
  • Protein tyrosine kinase 2 beta
KeywordsTRANSFERASE / four-helix bundle / LD4 motif
Function / homology
Function and homology information


regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / marginal zone B cell differentiation / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of myeloid cell differentiation ...regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / marginal zone B cell differentiation / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of myeloid cell differentiation / negative regulation of bone mineralization / cortical cytoskeleton organization / neuropilin binding / vinculin binding / 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 / microtubule associated complex / growth hormone receptor signaling pathway / 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 / Smooth Muscle Contraction / positive regulation of excitatory postsynaptic potential / GAB1 signalosome / vascular endothelial growth factor receptor signaling pathway / bone resorption / endothelial cell migration / cellular defense response / positive regulation of synaptic transmission, glutamatergic / postsynaptic density, intracellular component / regulation of cell adhesion / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / stress fiber / positive regulation of stress fiber assembly / cellular response to retinoic acid / ionotropic glutamate receptor binding / positive regulation of endothelial cell migration / ionotropic glutamate receptor signaling pathway / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / peptidyl-tyrosine phosphorylation / tumor necrosis factor-mediated signaling pathway / integrin-mediated signaling pathway / cellular response to reactive oxygen species / 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 / beta-catenin binding / regulation of synaptic plasticity / VEGFA-VEGFR2 Pathway / epidermal growth factor receptor signaling pathway / long-term synaptic potentiation / neuron migration / positive regulation of angiogenesis / cell-cell junction / cell migration / presynapse / regulation of cell shape / lamellipodium / protein autophosphorylation / growth cone / cell body / protein-containing complex assembly / protein tyrosine kinase activity / cell cortex / protein phosphatase binding / 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 / cell adhesion / 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
Similarity search - Function
Paxillin / : / : / Paxillin family / Nucleotidyltransferases domain 2 / 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 ...Paxillin / : / : / Paxillin family / Nucleotidyltransferases domain 2 / 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 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Paxillin / Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLulo, J.E. / Yuzawa, S. / Schlessinger, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structures of free and ligand-bound focal adhesion targeting domain of Pyk2
Authors: Lulo, J. / Yuzawa, S. / Schlessinger, J.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tyrosine kinase 2 beta
E: Paxillin
F: Paxillin
B: Protein tyrosine kinase 2 beta
C: Paxillin
D: Paxillin


Theoretical massNumber of molelcules
Total (without water)39,1316
Polymers39,1316
Non-polymers00
Water30617
1
A: Protein tyrosine kinase 2 beta
E: Paxillin
F: Paxillin


Theoretical massNumber of molelcules
Total (without water)19,5653
Polymers19,5653
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-15 kcal/mol
Surface area8660 Å2
MethodPISA
2
B: Protein tyrosine kinase 2 beta
C: Paxillin
D: Paxillin


Theoretical massNumber of molelcules
Total (without water)19,5653
Polymers19,5653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-18 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.774, 73.774, 156.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protein tyrosine kinase 2 beta


Mass: 16692.205 Da / Num. of mol.: 2
Fragment: Focal Adhesion Targeting (FAT) Domain, UNP residues 861-1009
Mutation: C899A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14289, non-specific protein-tyrosine kinase
#2: Protein/peptide
Paxillin


Mass: 1436.609 Da / Num. of mol.: 4 / Fragment: Paxillin LD4 Motif, UNP residues 262-274 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: P49023
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 4.1 M NaCl, 100 mM HEPES, 5% glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2005
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 9532 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.95→3.06 Å / % possible all: 80.3

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.4.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GM2

3gm2


Resolution: 2.95→42.67 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 20.693 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28986 459 4.8 %RANDOM
Rwork0.23312 ---
obs0.23586 9465 97.71 %-
all-9532 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.162 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2--1.38 Å20 Å2
3----2.77 Å2
Refinement stepCycle: LAST / Resolution: 2.95→42.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 0 17 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222528
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.352.023424
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3915322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.83326.117103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.29915488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0841516
X-RAY DIFFRACTIONr_chiral_restr0.080.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211800
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5131.51642
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0122646
X-RAY DIFFRACTIONr_scbond_it1.4153886
X-RAY DIFFRACTIONr_scangle_it2.684.5778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 23 -
Rwork0.281 505 -
obs--78.45 %

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