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- PDB-3b71: CD4 endocytosis motif bound to the Focal Adhesion Targeting (FAT)... -

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Basic information

Entry
Database: PDB / ID: 3b71
TitleCD4 endocytosis motif bound to the Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase
Components
  • Focal adhesion kinase 1
  • T-cell surface glycoprotein CD4
KeywordsPROTEIN BINDING / Four-helix bundle / protein-protein complex / ATP-binding / Cell junction / Kinase / Nucleotide-binding / Phosphorylation / Transferase / Tyrosine-protein kinase / Glycoprotein / Host-virus interaction / Immune response / Immunoglobulin domain / Lipoprotein / Membrane / Palmitate / Transmembrane
Function / homology
Function and homology information


netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of epithelial cell migration / maintenance of protein location in cell / detection of muscle stretch / T cell selection ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of epithelial cell migration / maintenance of protein location in cell / detection of muscle stretch / T cell selection / MHC class II protein binding / JUN kinase binding / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of macrophage proliferation / DCC mediated attractive signaling / positive regulation of fibroblast migration / regulation of T cell activation / Signal regulatory protein family interactions / Other interleukin signaling / regulation of GTPase activity / extracellular matrix structural constituent / growth hormone receptor signaling pathway / MET activates PTK2 signaling / regulation of focal adhesion assembly / negative regulation of cell-cell adhesion / T cell receptor complex / positive regulation of wound healing / p130Cas linkage to MAPK signaling for integrins / regulation of osteoblast differentiation / enzyme-linked receptor protein signaling pathway / Apoptotic cleavage of cellular proteins / establishment of cell polarity / positive regulation of macrophage chemotaxis / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of cytoskeleton organization / regulation of cell adhesion mediated by integrin / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of protein phosphorylation / macrophage differentiation / negative regulation of anoikis / regulation of calcium ion transport / Generation of second messenger molecules / T cell differentiation / positive regulation of epithelial cell migration / ephrin receptor signaling pathway / Co-inhibition by PD-1 / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / positive regulation of protein kinase activity / Binding and entry of HIV virion / vascular endothelial growth factor receptor signaling pathway / regulation of cell adhesion / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / stress fiber / coreceptor activity / EPHB-mediated forward signaling / Integrin signaling / protein tyrosine phosphatase activity / NCAM signaling for neurite out-growth / positive regulation of interleukin-2 production / transforming growth factor beta receptor signaling pathway / SH2 domain binding / positive regulation of calcium-mediated signaling / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / molecular function activator activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / integrin-mediated signaling pathway / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / Vpu mediated degradation of CD4 / non-specific protein-tyrosine kinase / cell motility / placenta development / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / peptidyl-tyrosine phosphorylation / Regulation of actin dynamics for phagocytic cup formation / positive regulation of T cell activation / VEGFA-VEGFR2 Pathway / epidermal growth factor receptor signaling pathway / MHC class II protein complex binding / integrin binding / transmembrane signaling receptor activity / Downstream TCR signaling / cell migration / Cargo recognition for clathrin-mediated endocytosis / regulation of cell shape
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 / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Immunoglobulin / Immunoglobulin domain / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
T-cell surface glycoprotein CD4 / Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsGarron, M.-L. / Arold, S.T.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural basis for the interaction between focal adhesion kinase and CD4.
Authors: Garron, M.L. / Arthos, J. / Guichou, J.F. / McNally, J. / Cicala, C. / Arold, S.T.
History
DepositionOct 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
D: T-cell surface glycoprotein CD4
E: T-cell surface glycoprotein CD4
F: T-cell surface glycoprotein CD4


Theoretical massNumber of molelcules
Total (without water)62,1846
Polymers62,1846
Non-polymers00
Water00
1
A: Focal adhesion kinase 1
D: T-cell surface glycoprotein CD4


Theoretical massNumber of molelcules
Total (without water)20,7282
Polymers20,7282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Focal adhesion kinase 1
E: T-cell surface glycoprotein CD4


Theoretical massNumber of molelcules
Total (without water)20,7282
Polymers20,7282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Focal adhesion kinase 1
F: T-cell surface glycoprotein CD4


Theoretical massNumber of molelcules
Total (without water)20,7282
Polymers20,7282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.071, 220.472, 97.546
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 / FADK 1 / pp125FAK / Protein- tyrosine kinase 2


Mass: 17949.697 Da / Num. of mol.: 3 / Fragment: Focal Adhesion Targeting domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2, FAK, FAK1 / Plasmid: pGEX-6P2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q05397, non-specific protein-tyrosine kinase
#2: Protein/peptide T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 2778.303 Da / Num. of mol.: 3 / Fragment: residues 403-425 / Source method: obtained synthetically / References: UniProt: P01730

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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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3.9 M NaCl, 2.5 % glycerol, 100 mM Hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97982 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 16, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97982 Å / Relative weight: 1
ReflectionResolution: 2.81→29 Å / Num. all: 21922 / Num. obs: 21922 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.143 / Rsym value: 0.112 / Net I/σ(I): 9.2
Reflection shellResolution: 2.81→2.97 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.543 / % possible all: 69.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K05

1k05


Resolution: 2.82→29 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.894 / SU B: 34.901 / SU ML: 0.306 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30712 459 2.1 %RANDOM
Rwork0.24053 ---
obs0.24195 21463 93.83 %-
all-21463 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.107 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---0.15 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.82→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 0 0 3448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223494
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8522.0154721
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.375437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89826.103136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.52715705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5951517
X-RAY DIFFRACTIONr_chiral_restr0.1110.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022479
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2810.21886
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.22425
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9131.52298
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21523610
X-RAY DIFFRACTIONr_scbond_it2.08931323
X-RAY DIFFRACTIONr_scangle_it3.4234.51111
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.82→2.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.529 24 -
Rwork0.37 963 -
obs--58.89 %
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)
14.4509-3.51040.80775.5594-1.29353.68030.06060.0141-0.19260.0639-0.07170.330.5101-0.11660.01110.1741-0.0894-0.02970.1188-0.06240.129329.410926.791433.2015
22.1383-1.7842-0.77185.67682.42633.8291-0.0141-0.184-0.09220.30750.1325-0.3073-0.12260.0321-0.1184-0.0442-0.0178-0.04780.1960.01250.10646.20165.034636.8913
33.6923-4.35720.876210.819-1.49722.3802-0.0932-0.20320.1070.18170.2918-0.7691-0.49680.1746-0.19860.3262-0.06720.02730.2964-0.07610.20059.723793.501734.369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA916 - 104926 - 159
2X-RAY DIFFRACTION1DD406 - 4164 - 14
3X-RAY DIFFRACTION2BB909 - 104719 - 157
4X-RAY DIFFRACTION2EE406 - 4164 - 14
5X-RAY DIFFRACTION3CC909 - 104719 - 157
6X-RAY DIFFRACTION3FF408 - 4166 - 14

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