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- PDB-3ml4: Crystal structure of a complex between Dok7 PH-PTB and the MuSK j... -

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Basic information

Entry
Database: PDB / ID: 3ml4
TitleCrystal structure of a complex between Dok7 PH-PTB and the MuSK juxtamembrane region
Components
  • Muscle, skeletal receptor tyrosine-protein kinase
  • Protein Dok-7
KeywordsSIGNALING PROTEIN / tyrosine phosphorylation / adapter protein / dimerization
Function / homology
Function and homology information


positive regulation of protein geranylgeranylation / regulation of synaptic assembly at neuromuscular junction / protein tyrosine kinase collagen receptor activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / positive regulation of synaptic transmission, cholinergic / positive regulation of skeletal muscle acetylcholine-gated channel clustering / multicellular organism development / positive regulation of kinase activity / neuromuscular junction development ...positive regulation of protein geranylgeranylation / regulation of synaptic assembly at neuromuscular junction / protein tyrosine kinase collagen receptor activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / positive regulation of synaptic transmission, cholinergic / positive regulation of skeletal muscle acetylcholine-gated channel clustering / multicellular organism development / positive regulation of kinase activity / neuromuscular junction development / receptor clustering / plasma membrane => GO:0005886 / positive regulation of protein tyrosine kinase activity / response to electrical stimulus / cell surface receptor protein tyrosine kinase signaling pathway / collagen binding / transmembrane receptor protein tyrosine kinase activity / phosphatidylinositol binding / cell projection / PDZ domain binding / long-term synaptic potentiation / neuromuscular junction / receptor protein-tyrosine kinase / memory / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / postsynaptic membrane / protein tyrosine kinase activity / protein autophosphorylation / cell differentiation / receptor complex / positive regulation of protein phosphorylation / external side of plasma membrane / negative regulation of gene expression / synapse / positive regulation of gene expression / regulation of DNA-templated transcription / protein kinase binding / mitochondrion / nucleoplasm / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Protein Dok-7 / Dok-7, PH domain / Dok-7, PTB domain / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. ...Protein Dok-7 / Dok-7, PH domain / Dok-7, PTB domain / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Roll / 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 / Mainly Beta
Similarity search - Domain/homology
Protein Dok-7 / Muscle, skeletal receptor tyrosine-protein kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsBergamin, E. / Hubbard, S.R.
CitationJournal: Mol.Cell / Year: 2010
Title: The Cytoplasmic Adaptor Protein Dok7 Activates the Receptor Tyrosine Kinase MuSK via Dimerization.
Authors: Bergamin, E. / Hallock, P.T. / Burden, S.J. / Hubbard, S.R.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Dok-7
B: Protein Dok-7
C: Protein Dok-7
D: Protein Dok-7
E: Muscle, skeletal receptor tyrosine-protein kinase
F: Muscle, skeletal receptor tyrosine-protein kinase
G: Muscle, skeletal receptor tyrosine-protein kinase
H: Muscle, skeletal receptor tyrosine-protein kinase


Theoretical massNumber of molelcules
Total (without water)107,4178
Polymers107,4178
Non-polymers00
Water1,26170
1
A: Protein Dok-7
B: Protein Dok-7
E: Muscle, skeletal receptor tyrosine-protein kinase
F: Muscle, skeletal receptor tyrosine-protein kinase


Theoretical massNumber of molelcules
Total (without water)53,7084
Polymers53,7084
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-34 kcal/mol
Surface area18660 Å2
MethodPISA
2
C: Protein Dok-7
D: Protein Dok-7
G: Muscle, skeletal receptor tyrosine-protein kinase
H: Muscle, skeletal receptor tyrosine-protein kinase


Theoretical massNumber of molelcules
Total (without water)53,7084
Polymers53,7084
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-32 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.600, 134.600, 121.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Protein Dok-7 / Downstream of tyrosine kinase 7


Mass: 25100.234 Da / Num. of mol.: 4 / Fragment: UNP Residues 1-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dok7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q18PE0
#2: Protein/peptide
Muscle, skeletal receptor tyrosine-protein kinase / Muscle-specific tyrosine-protein kinase receptor / Muscle-specific kinase receptor / MuSK


Mass: 1753.959 Da / Num. of mol.: 4 / Fragment: UNP Residues 544-556 / Source method: obtained synthetically / Details: Peptide (12MER) / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q61006
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.7 M Na-K tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97854 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 39533 / % possible obs: 100 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.837 / SU B: 11.941 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30222 1981 5 %RANDOM
Rwork0.25268 ---
obs0.25518 37533 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 0 70 6712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226807
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.9719246
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78922.088273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.66151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9361556
X-RAY DIFFRACTIONr_chiral_restr0.0680.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025132
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.22897
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24514
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7211.54386
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.66226831
X-RAY DIFFRACTIONr_scbond_it1.08532789
X-RAY DIFFRACTIONr_scangle_it1.5054.52415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 148 -
Rwork0.305 2738 -
obs--100 %

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