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- PDB-3zdt: Crystal structure of basic patch mutant FAK FERM domain FAK31- 40... -

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Basic information

Entry
Database: PDB / ID: 3zdt
TitleCrystal structure of basic patch mutant FAK FERM domain FAK31- 405 K216A, K218A, R221A, K222A
ComponentsFOCAL ADHESION KINASE 1
KeywordsTRANSFERASE / CELL ADHESION
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / negative regulation of protein autophosphorylation / radial glia-guided pyramidal neuron migration / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / negative regulation of protein autophosphorylation / radial glia-guided pyramidal neuron migration / 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 / signal complex assembly / response to pH / angiogenesis involved in wound healing / wound healing, spreading of cells / positive regulation of protein tyrosine kinase activity / negative regulation of anoikis / negative regulation of cell-substrate adhesion / positive regulation of focal adhesion assembly / positive regulation of protein binding / regulation of cell adhesion / response to muscle stretch / molecular function activator activity / actin filament organization / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / sarcolemma / integrin binding / epidermal growth factor receptor signaling pathway / protein autophosphorylation / protease binding / protein tyrosine kinase activity / cell cortex / positive regulation of cell migration / ciliary basal body / focal adhesion / positive regulation of cell population proliferation / centrosome / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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) / PH-domain like / FERM central domain / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Ubiquitin-like domain superfamily / 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: 3.15 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
DepositionNov 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: 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)85,7972
Polymers85,7972
Non-polymers00
Water1267
1
A: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)42,8991
Polymers42,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FOCAL ADHESION KINASE 1


Theoretical massNumber of molelcules
Total (without water)42,8991
Polymers42,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.567, 175.527, 60.032
Angle α, β, γ (deg.)90.00, 93.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42898.531 Da / Num. of mol.: 2 / Fragment: FERM DOMAIN, RESIDUES 31-405 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q00944, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsK216A, K218A, R221A, K222A

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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: 2.54 Å3/Da / Density % sol: 51.6 % / Description: NONE
Crystal growpH: 8.5
Details: 14% PEG4K, 200 MM MGCL2, 100 MM TRIS PH 8.5, 10 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.07214
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07214 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 14023 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.77 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5
Reflection shellResolution: 3.15→3.34 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AL6

2al6


Resolution: 3.15→43.88 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.881 / SU B: 62.884 / SU ML: 0.482 / Cross valid method: THROUGHOUT / ESU R Free: 0.543 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27822 739 5 %RANDOM
Rwork0.21427 ---
obs0.21745 14023 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å2-0.05 Å2
2--0.27 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.15→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 0 7 5192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225296
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9587163
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.825638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.34724.231260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44615937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2781534
X-RAY DIFFRACTIONr_chiral_restr0.1070.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214008
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_it0.5831.53206
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12825180
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.42532090
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5194.51983
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: 3.151→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 54 -
Rwork0.326 1020 -
obs--97.55 %
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)
113.50462.4974-2.529212.2352-1.97198.71740.0736-0.1678-1.63940.1325-0.06260.86540.8986-0.157-0.0110.31220.0027-0.15860.09010.00790.4178-3.258-15.7194.2
21.8111-0.28593.16521.8228-0.01218.50970.24330.71590.0753-0.6935-0.2313-0.34530.21561.5471-0.0120.48990.02810.09210.48980.04960.35825.57-1.175-17.193
310.1819-2.8436-0.09897.18610.91226.5462-0.0717-0.4075-0.3238-0.13580.21920.63490.20320.0545-0.14760.1364-0.1418-0.01340.18380.00960.1597-12.0214.90912.27
412.58530.93733.57639.30723.22689.0015-0.3125-0.02491.37740.20880.0494-0.7118-1.35040.00140.26310.47270.02590.06090.07190.10480.45673.8745.7640.68
54.87640.5525-6.29222.30181.115418.95870.43731.1235-0.1128-0.7914-0.41850.2253-0.5391-1.8658-0.01880.72150.1592-0.04070.5249-0.01330.3835-0.88431.05-21.716
67.9437-2.78481.14117.5969-1.11723.8702-0.3929-0.34750.18510.44540.519-0.4645-0.3743-0.1675-0.12610.2822-0.11190.04250.21670.02380.162112.64825.94610.241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 128
2X-RAY DIFFRACTION2A129 - 254
3X-RAY DIFFRACTION3A255 - 363
4X-RAY DIFFRACTION4B33 - 128
5X-RAY DIFFRACTION5B129 - 254
6X-RAY DIFFRACTION6B255 - 363

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