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- PDB-6bz3: Complex structure of FAK FAT domain and DCC P3 motif -

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Basic information

Entry
Database: PDB / ID: 6bz3
TitleComplex structure of FAK FAT domain and DCC P3 motif
Components
  • Focal adhesion kinase 1
  • Netrin receptor DCC
KeywordsTRANSFERASE/MEMBRANE PROTEIN / 4-helix bundle / axon guidance / focal adhesion kinase / transferase-peptide complex / MEMBRANE PROTEIN / TRANSFERASE-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / DCC mediated attractive signaling / anterior/posterior axon guidance / Apoptotic cleavage of cellular proteins / MET activates PTK2 signaling / netrin receptor activity ...Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / DCC mediated attractive signaling / anterior/posterior axon guidance / Apoptotic cleavage of cellular proteins / MET activates PTK2 signaling / netrin receptor activity / NCAM signaling for neurite out-growth / negative regulation of synapse assembly / negative regulation of axonogenesis / regulation of substrate adhesion-dependent cell spreading / central nervous system neuron axonogenesis / RHO GTPases Activate WASPs and WAVEs / EPHB-mediated forward signaling / negative regulation of organ growth / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / intracellular chloride ion homeostasis / Extra-nuclear estrogen signaling / corpus callosum development / optic nerve development / RAF/MAP kinase cascade / regulation of epithelial cell migration / growth cone membrane / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell-cell adhesion mediated by integrin / regulation of modification of postsynaptic actin cytoskeleton / JUN kinase binding / VEGFA-VEGFR2 Pathway / blood vessel development / signal complex assembly / positive regulation of glial cell proliferation / regulation of cell adhesion mediated by integrin / negative regulation of cell adhesion mediated by integrin / positive regulation of macrophage proliferation / positive regulation of fibroblast migration / negative regulation of cell-cell adhesion / peptidyl-tyrosine autophosphorylation / positive regulation of smooth muscle cell migration / positive regulation of ubiquitin-dependent protein catabolic process / growth hormone receptor signaling pathway / regulation of focal adhesion assembly / nuclear migration / positive regulation of cardiac muscle hypertrophy / regulation of osteoblast differentiation / positive regulation of wound healing / axon development / positive regulation of macrophage chemotaxis / vasculogenesis / positive regulation of epithelial cell migration / negative regulation of anoikis / ephrin receptor signaling pathway / cellular response to transforming growth factor beta stimulus / regulation of cell adhesion / intercalated disc / transforming growth factor beta receptor signaling pathway / ciliary tip / JNK cascade / endothelial cell migration / positive regulation of epithelial to mesenchymal transition / postsynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission / extracellular matrix organization / phosphatase binding / phosphatidylinositol 3-kinase binding / stress fiber / response to amphetamine / peptidyl-tyrosine phosphorylation / protein tyrosine phosphatase activity / SH2 domain binding / positive regulation of smooth muscle cell proliferation / positive regulation of phagocytosis / positive regulation of cell adhesion / axon guidance / integrin-mediated signaling pathway / negative regulation of cell migration / negative regulation of autophagy / molecular function activator activity / positive regulation of neuron projection development / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / neuron migration / cell-cell adhesion / cerebral cortex development / regulation of cell shape / vasodilation / microtubule cytoskeleton organization / sarcolemma / postsynaptic density membrane / integrin binding / Schaffer collateral - CA1 synapse / epidermal growth factor receptor signaling pathway / angiogenesis / MAPK cascade / cilium
Similarity search - Function
Neogenin, C-terminal / Neogenin C-terminus / 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 / : ...Neogenin, C-terminal / Neogenin C-terminus / 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 / Immunoglobulin 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 / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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 / Netrin receptor DCC
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsXu, S. / Wang, J.-H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL103526 United States
CitationJournal: Cell Discov / Year: 2018
Title: The binding of DCC-P3 motif and FAK-FAT domain mediates the initial step of netrin-1/DCC signaling for axon attraction.
Authors: Xu, S. / Liu, Y. / Li, X. / Liu, Y. / Meijers, R. / Zhang, Y. / Wang, J.H.
History
DepositionDec 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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: Netrin receptor DCC
C: Focal adhesion kinase 1
D: Netrin receptor DCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9585
Polymers32,9184
Non-polymers401
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-77 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.178, 36.130, 65.429
Angle α, β, γ (deg.)90.000, 104.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Focal adhesion kinase 1 / FADK 1 / Focal adhesion kinase-related nonkinase / FRNK / Protein-tyrosine kinase 2 / p125FAK / pp125FAK


Mass: 14006.386 Da / Num. of mol.: 2 / Fragment: FAT domain residues 959-1084
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptk2, Fadk, Fak, Fak1, Kiaa4203 / Plasmid: pET28Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P34152, non-specific protein-tyrosine kinase
#2: Protein/peptide Netrin receptor DCC / Tumor suppressor protein DCC


Mass: 2452.735 Da / Num. of mol.: 2 / Fragment: P3 motif residues 1421-1443 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q63155
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris pH8.5, 20% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.497→50 Å / Num. obs: 10318 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.2
Reflection shellResolution: 2.497→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2 / Num. unique obs: 978 / % possible all: 93.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OW6

1ow6


Resolution: 2.497→39.889 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.88
RfactorNum. reflection% reflection
Rfree0.2686 496 4.81 %
Rwork0.226 --
obs0.2278 10314 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.84 Å2 / Biso mean: 64.3044 Å2 / Biso min: 29.89 Å2
Refinement stepCycle: final / Resolution: 2.497→39.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 1 12 2230
Biso mean--81.48 53.76 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062243
X-RAY DIFFRACTIONf_angle_d0.5733017
X-RAY DIFFRACTIONf_chiral_restr0.03371
X-RAY DIFFRACTIONf_plane_restr0.005381
X-RAY DIFFRACTIONf_dihedral_angle_d17.7111433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4974-2.74870.32051250.28962336246195
2.7487-3.14630.34281260.297824462572100
3.1463-3.96340.2581300.231424722602100
3.9634-39.89440.23551150.190625642679100
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)
12.8764-0.4676-1.86241.32811.65423.55590.3230.0486-0.0287-0.0408-0.4711-0.59830.36750.44860.01190.45220.0895-0.03340.43090.09590.3948-25.38165.177826.1822
23.0832-0.979-0.59973.26420.22652.69420.21830.2834-0.0437-0.2031-0.07650.1487-0.1201-0.2097-0.14670.338-0.01520.04640.3024-0.0180.3401-6.3982-1.46687.4161
31.9281-0.3224-1.01286.4448-2.3642.539-0.02190.0715-0.78190.0002-0.40340.48990.6495-0.64420.16720.57190.00120.02760.6008-0.0090.8669-20.7631-6.64819.666
43.7667-2.0487-1.36631.46411.63562.1801-0.2505-0.3579-0.1450.09310.2332-0.2337-0.0779-0.5156-0.06240.46720.02590.03940.30530.0310.4139-14.8693-2.505914.7046
52.87210.53191.46211.9711.21884.31340.3136-0.1172-0.1614-0.016-0.08240.07670.3353-1.30440.04980.4114-0.0282-0.00530.57810.02150.396-36.05276.024829.8777
63.97930.8827-1.27511.78621.81695.90850.2220.85610.5353-0.6624-0.6999-1.1484-0.90860.8612-0.15660.7001-0.07980.19450.7576-0.02320.6969-23.75114.296924.9765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 922 through 946 )A922 - 946
2X-RAY DIFFRACTION2chain 'A' and (resid 947 through 1046 )A947 - 1046
3X-RAY DIFFRACTION3chain 'B' and (resid 1423 through 1440 )B0
4X-RAY DIFFRACTION4chain 'C' and (resid 922 through 946 )C922 - 946
5X-RAY DIFFRACTION5chain 'C' and (resid 947 through 1046 )C947 - 1046
6X-RAY DIFFRACTION6chain 'D' and (resid 1423 through 1441 )D0

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