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- PDB-1luf: Crystal Structure of the MuSK Tyrosine Kinase: Insights into Rece... -

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Basic information

Entry
Database: PDB / ID: 1luf
TitleCrystal Structure of the MuSK Tyrosine Kinase: Insights into Receptor Autoregulation
Componentsmuscle-specific tyrosine kinase receptor musk
KeywordsTRANSFERASE / phosphorylation / signal transduction / mass spectrometry
Function / homology
Function and homology information


positive regulation of protein geranylgeranylation / positive regulation of synaptic assembly at neuromuscular junction / regulation of synaptic assembly at neuromuscular junction / positive regulation of motor neuron apoptotic process / skeletal muscle acetylcholine-gated channel clustering / positive regulation of synaptic transmission, cholinergic / positive regulation of skeletal muscle acetylcholine-gated channel clustering / Wnt-protein binding / motor neuron apoptotic process / neuromuscular junction development ...positive regulation of protein geranylgeranylation / positive regulation of synaptic assembly at neuromuscular junction / regulation of synaptic assembly at neuromuscular junction / positive regulation of motor neuron apoptotic process / skeletal muscle acetylcholine-gated channel clustering / positive regulation of synaptic transmission, cholinergic / positive regulation of skeletal muscle acetylcholine-gated channel clustering / Wnt-protein binding / motor neuron apoptotic process / neuromuscular junction development / response to muscle activity / enzyme-linked receptor protein signaling pathway / cochlea development / receptor clustering / positive regulation of Rac protein signal transduction / response to axon injury / response to electrical stimulus / transmembrane receptor protein tyrosine kinase activity / cell projection / PDZ domain binding / long-term synaptic potentiation / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / GPI-linked ephrin receptor activity / transmembrane-ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / neuromuscular junction / receptor protein-tyrosine kinase / positive regulation of neuron projection development / memory / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / retina development in camera-type eye / protein tyrosine kinase activity / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / postsynaptic membrane / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / external side of plasma membrane / negative regulation of gene expression / synapse / positive regulation of gene expression / regulation of DNA-templated transcription / protein kinase binding / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain ...Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Immunoglobulin I-set / Immunoglobulin I-set 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 / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Immunoglobulin-like domain superfamily / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Muscle, skeletal receptor tyrosine protein kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTill, J.H. / Becerra, M. / Watty, A. / Lu, Y. / Ma, Y. / Neubert, T.A. / Burden, S.J. / Hubbard, S.R.
CitationJournal: Structure / Year: 2002
Title: Crystal structure of the MuSK tyrosine kinase: insights into receptor autoregulation.
Authors: Till, J.H. / Becerra, M. / Watty, A. / Lu, Y. / Ma, Y. / Neubert, T.A. / Burden, S.J. / Hubbard, S.R.
History
DepositionMay 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: muscle-specific tyrosine kinase receptor musk


Theoretical massNumber of molelcules
Total (without water)38,7551
Polymers38,7551
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.939, 146.939, 39.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein muscle-specific tyrosine kinase receptor musk


Mass: 38754.656 Da / Num. of mol.: 1 / Fragment: cytoplasmic region (residues 526-868)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q62838, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, HEPES, glycerol, TCEP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
20.75 Mammonium sulfate1reservoir
30.1 MHEPES1reservoirpH7.0
42 %glycerol1reservoir
51.3 mMTCEP1reservoir
60.1 Msodium thiocyanate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 29, 2001
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→28 Å / Num. all: 28438 / Num. obs: 25737 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 14.1 Å2
Reflection shellResolution: 2.05→2.1 Å / % possible all: 99
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 28438 / Num. measured all: 216370 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.319

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
MADNESSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1IRK

1irk


Resolution: 2.05→26.31 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1263 4.9 %RANDOM
Rwork0.231 ---
obs0.231 25736 96.8 %-
all-28438 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.431 Å2 / ksol: 0.359255 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2--1.48 Å20 Å2
3----2.96 Å2
Refine analyzeLuzzati coordinate error free: 0.3 Å / Luzzati sigma a free: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.05→26.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 0 114 2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.741.5
X-RAY DIFFRACTIONc_mcangle_it1.342
X-RAY DIFFRACTIONc_scbond_it3.412
X-RAY DIFFRACTIONc_scangle_it4.212.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 206 5.1 %
Rwork0.27 3872 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2DNA-RNA.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3WATER_REP.PARAM&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4ION.PARAM&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5PARAMCSDX.MISC&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 25737 / % reflection Rfree: 5 % / Rfactor obs: 0.231 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Lowest resolution: 2.1 Å / Rfactor Rfree: 0.313 / Rfactor Rwork: 0.27

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