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- PDB-4cye: Crystal structure of avian FAK FERM domain FAK31-405 at 3.2A -

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Basic information

Entry
Database: PDB / ID: 4cye
TitleCrystal structure of avian FAK FERM domain FAK31-405 at 3.2A
ComponentsFOCAL ADHESION KINASE 1PTK2
KeywordsTRANSFERASE / FAK / FERM DOMAIN / CELL ADHESION
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / angiogenesis involved in wound healing / signal complex assembly / response to pH / negative regulation of cell-substrate adhesion / wound healing, spreading of cells / positive regulation of focal adhesion assembly / negative regulation of anoikis / positive regulation of protein tyrosine kinase activity / regulation of cell adhesion / response to muscle stretch / ciliary basal body / actin filament organization / molecular function activator activity / non-specific protein-tyrosine kinase / sarcolemma / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / integrin binding / cell cortex / positive regulation of protein binding / angiogenesis / protein tyrosine kinase activity / protease binding / dendritic spine / protein autophosphorylation / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Acyl-CoA Binding Protein - #10 / 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 / Acyl-CoA Binding Protein ...Acyl-CoA Binding Protein - #10 / 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 / Acyl-CoA Binding Protein / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / 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 / Roll / Roll / 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Focal adhesion kinase 1
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGoni, G.M. / Epifano, C. / Boskovic, J. / Camacho-Artacho, M. / Zhou, J. / Martin, M.T. / Eck, M.J. / Kremer, L. / Graeter, F. / Gervasio, F.L. ...Goni, G.M. / Epifano, C. / Boskovic, J. / Camacho-Artacho, M. / Zhou, J. / Martin, M.T. / Eck, M.J. / Kremer, L. / Graeter, F. / Gervasio, F.L. / Perez-Moreno, M. / Lietha, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Phosphatidylinositol 4,5-Bisphosphate Triggers Activation of Focal Adhesion Kinase by Inducing Clustering and Conformational Changes.
Authors: Goni, G.M. / Epifano, C. / Boskovic, J. / Camacho-Artacho, M. / Zhou, J. / Bronowska, A. / Martin, M.T. / Eck, M.J. / Kremer, L. / Grater, F. / Gervasio, F.L. / Perez-Moreno, M. / Lietha, D.
History
DepositionApr 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)86,0302
Polymers86,0302
Non-polymers00
Water82946
1
A: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)43,0151
Polymers43,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)43,0151
Polymers43,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.934, 146.128, 69.052
Angle α, β, γ (deg.)90.00, 96.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FOCAL ADHESION KINASE 1 / PTK2 / FADK 1 / FOCAL ADHESION KINASE-RELATED NONKINASE / FRNK / P41/ P43FRNK / PROTEIN-TYROSINE KINASE 2 ...FADK 1 / FOCAL ADHESION KINASE-RELATED NONKINASE / FRNK / P41/ P43FRNK / PROTEIN-TYROSINE KINASE 2 / P125FAK / PP125FAK / FAK


Mass: 43014.824 Da / Num. of mol.: 2 / Fragment: FERM, RESIDUES 31-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q00944, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.56 Å3/Da / Density % sol: 51.91 % / Description: NONE
Crystal growpH: 8.5
Details: 18%PEG4000, 325MM MGCL2, 0.1M TRIS PH8.5, 10MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99988
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 3.2→73 Å / Num. obs: 13590 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AEH

2aeh


Resolution: 3.2→73.06 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.883 / SU B: 46.802 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23977 699 4.9 %RANDOM
Rwork0.17304 ---
obs0.17633 13590 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.567 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20.26 Å2
2---0.4 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 3.2→73.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5385 0 0 46 5431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195498
X-RAY DIFFRACTIONr_bond_other_d0.0010.025298
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9627420
X-RAY DIFFRACTIONr_angle_other_deg0.702312197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08224.17271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9881538
X-RAY DIFFRACTIONr_chiral_restr0.0610.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021285
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_it1.6843.7722653
X-RAY DIFFRACTIONr_mcbond_other1.6823.7712652
X-RAY DIFFRACTIONr_mcangle_it2.9525.6483311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5563.8952845
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 51 -
Rwork0.229 1008 -
obs--100 %
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)
13.8737-4.2349-0.71568.68981.86922.14270.0125-0.1957-0.10990.2525-0.06250.01260.2207-0.17850.04990.0618-0.0958-0.03190.18080.06390.0446.65693.01436.125
21.9343-0.7749-1.25531.53761.90868.40880.1365-0.24950.28870.18810.1584-0.2286-0.05450.3033-0.29490.07360.0096-0.01860.1611-0.04320.1283.472115.27151.867
35.56451.2909-2.14412.2995-0.62113.72220.05330.0591-0.1039-0.0226-0.0578-0.4407-0.05370.04420.00440.06650.0487-0.02590.12-0.03070.133216.622107.68620.147
47.9098-2.50891.61356.1767-2.24916.3090.00510.63950.8281-0.4444-0.01890.2992-0.69040.01820.01380.2115-0.0187-0.06330.13150.05820.16340.745145.7157.744
54.41560.8011.33764.48212.78665.14620.0589-0.3403-0.110.6138-0.22090.12480.2345-0.27340.1620.0975-0.00710.00730.0718-0.01390.02988.248142.24134.259
64.36271.1588-0.63573.4124-1.05574.8694-0.1699-0.07860.19460.18140.20650.0935-0.1757-0.2026-0.03660.06140.0664-0.04560.0751-0.05120.0584-9.503124.13810.43
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 129
2X-RAY DIFFRACTION2A130 - 253
3X-RAY DIFFRACTION3A254 - 360
4X-RAY DIFFRACTION4B33 - 129
5X-RAY DIFFRACTION5B130 - 253
6X-RAY DIFFRACTION6B254 - 360

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