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- PDB-1k05: Crystal structure of the Focal Adhesion Targeting Domain of Focal... -

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Basic information

Entry
Database: PDB / ID: 1k05
TitleCrystal structure of the Focal Adhesion Targeting Domain of Focal Adhesion Kinase
ComponentsFOCAL ADHESION KINASE 1PTK2
KeywordsTRANSFERASE / up-down-up-down four helical bundle
Function / homology
Function and homology information


netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration / DCC mediated attractive signaling / Signal regulatory protein family interactions / growth hormone receptor signaling pathway / regulation of osteoblast differentiation / regulation of cytoskeleton organization / MET activates PTK2 signaling / regulation of focal adhesion assembly / establishment of cell polarity / positive regulation of wound healing / positive regulation of macrophage chemotaxis / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / negative regulation of cell-cell adhesion / Apoptotic cleavage of cellular proteins / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / positive regulation of epithelial to mesenchymal transition / ephrin receptor signaling pathway / positive regulation of protein kinase activity / vascular endothelial growth factor receptor signaling pathway / regulation of cell adhesion / heart morphogenesis / stress fiber / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / SH2 domain binding / Integrin signaling / transforming growth factor beta receptor signaling pathway / ciliary basal body / placenta development / protein tyrosine phosphatase activity / molecular function activator activity / cell motility / integrin-mediated signaling pathway / axon guidance / FCGR3A-mediated phagocytosis / regulation of protein phosphorylation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cell migration / integrin binding / actin binding / regulation of cell population proliferation / cell cortex / regulation of cell shape / RAF/MAP kinase cascade / protein phosphatase binding / angiogenesis / protein tyrosine kinase activity / dendritic spine / Extra-nuclear estrogen signaling / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / positive regulation of protein phosphorylation / focal adhesion / intracellular membrane-bounded organelle / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single helix bin / 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 ...Single helix bin / 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 / FERM domain signature 2. / 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) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.9 Å
AuthorsArold, S.T. / Hoellerer, M.K. / Noble, M.E.M.
CitationJournal: Structure / Year: 2002
Title: The structural basis of localization and signaling by the focal adhesion targeting domain.
Authors: Arold, S.T. / Hoellerer, M.K. / Noble, M.E.
History
DepositionSep 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FOCAL ADHESION KINASE 1
B: FOCAL ADHESION KINASE 1
C: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)53,8493
Polymers53,8493
Non-polymers00
Water1086
1
A: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)17,9501
Polymers17,9501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)17,9501
Polymers17,9501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)17,9501
Polymers17,9501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: FOCAL ADHESION KINASE 1
B: FOCAL ADHESION KINASE 1

A: FOCAL ADHESION KINASE 1
B: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)71,7994
Polymers71,7994
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4730 Å2
ΔGint-32 kcal/mol
Surface area28480 Å2
MethodPISA
5
C: FOCAL ADHESION KINASE 1

C: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)35,8992
Polymers35,8992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1780 Å2
ΔGint-15 kcal/mol
Surface area15500 Å2
MethodPISA
6
B: FOCAL ADHESION KINASE 1
C: FOCAL ADHESION KINASE 1

B: FOCAL ADHESION KINASE 1
C: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)71,7994
Polymers71,7994
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6100 Å2
ΔGint-43 kcal/mol
Surface area28160 Å2
MethodPISA
7
B: FOCAL ADHESION KINASE 1

B: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)35,8992
Polymers35,8992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1780 Å2
ΔGint-15 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.484, 222.101, 97.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein FOCAL ADHESION KINASE 1 / PTK2 / FADK 1


Mass: 17949.697 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAK / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q05397, EC: 2.7.1.112
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.42 Å3/Da / Density % sol: 71.95 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Hepes, NaCl, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-HCl1droppH8.0
2150 mM1dropNaCl
32 mMEDTA1drop
42 mMdithiothreitol1drop
520 mg/mlprotein1drop
6100 mMHEPES1reservoirpH7.0
73.3 M1reservoirNaCl
81 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.9→31.3 Å / Num. obs: 20719 / % possible obs: 96.9 % / Observed criterion σ(F): 0.9 / Observed criterion σ(I): 0.9 / Redundancy: 2.4 % / Biso Wilson estimate: 90 Å2 / Rsym value: 0.069 / Net I/σ(I): 7.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 4413 / Rsym value: 0.626 / % possible all: 94.9
Reflection
*PLUS
Num. measured all: 48770 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 94.9 % / Rmerge(I) obs: 0.626

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.9→31.3 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1000 -RANDOM
Rwork0.245 ---
all-21585 --
obs-21585 96.9 %-
Displacement parametersBiso mean: 76.8 Å2
Baniso -1Baniso -2Baniso -3
1--34.889 Å20 Å20 Å2
2--18.4 Å20 Å2
3---16.489 Å2
Refinement stepCycle: LAST / Resolution: 2.9→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 0 6 3257
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellResolution: 2.9→2.95 Å
RfactorNum. reflection% reflection
Rfree0.511 39 -
Rwork0.503 --
obs-956 92.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
Refinement
*PLUS
% reflection Rfree: 7 % / Rfactor obs: 0.245 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.511 / Rfactor Rwork: 0.503 / Rfactor obs: 0.503

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