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- PDB-3hkl: Crystal Structure of the Frizzled-like Cysteine-rich Domain of MuSK -

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Basic information

Entry
Database: PDB / ID: 3hkl
TitleCrystal Structure of the Frizzled-like Cysteine-rich Domain of MuSK
ComponentsMuscle, skeletal receptor tyrosine protein kinaseSkeletal muscle
KeywordsTransferase / Signaling protein / MuSK / RECEPTOR TYROSINE KINASE / FRIZZLED CRD / ATP-binding / Disulfide bond / Glycoprotein / Immunoglobulin domain / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


positive regulation of protein geranylgeranylation / regulation of synaptic assembly at neuromuscular junction / positive 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 / response to muscle activity / motor neuron apoptotic process ...positive regulation of protein geranylgeranylation / regulation of synaptic assembly at neuromuscular junction / positive 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 / response to muscle activity / motor neuron apoptotic process / neuromuscular junction development / cochlea development / enzyme-linked receptor protein signaling pathway / 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 / cell surface receptor protein tyrosine kinase signaling pathway / neuromuscular junction / receptor protein-tyrosine kinase / memory / positive regulation of neuron projection development / positive regulation of peptidyl-tyrosine phosphorylation / retina development in camera-type eye / postsynaptic membrane / protein tyrosine kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / receptor complex / positive regulation of protein phosphorylation / phosphorylation / external side of plasma membrane / negative regulation of gene expression / synapse / regulation of DNA-templated transcription / positive regulation of gene expression / protein kinase binding / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Frizzled cysteine-rich domain / Frizzled cysteine-rich 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 ...Frizzled cysteine-rich domain / Frizzled cysteine-rich 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Muscle, skeletal receptor tyrosine protein kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsStiegler, A.L. / Hubbard, S.R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the frizzled-like cysteine-rich domain of the receptor tyrosine kinase MuSK.
Authors: Stiegler, A.L. / Burden, S.J. / Hubbard, S.R.
History
DepositionMay 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muscle, skeletal receptor tyrosine protein kinase
B: Muscle, skeletal receptor tyrosine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6254
Polymers43,7762
Non-polymers8492
Water1,13563
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-17 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.592, 44.422, 69.530
Angle α, β, γ (deg.)90.00, 108.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Muscle, skeletal receptor tyrosine protein kinase / Skeletal muscle / Muscle-specific kinase receptor / MuSK


Mass: 21888.062 Da / Num. of mol.: 2 / Fragment: FZ-CRD, residues 313-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Musk / Plasmid: PACGP67 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q62838, receptor protein-tyrosine kinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG 4000, 0.2M SODIUM ACETATE, 0.1M TRIS PH 8.5, 5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9787 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.1→34.47 Å / Num. all: 22374 / Num. obs: 22050
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.299 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→34.47 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.892 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26433 1129 5.1 %RANDOM
Rwork0.22619 ---
obs0.22822 20869 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.338 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å21.91 Å2
2--0.84 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 56 63 2349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0682.0083243
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4835291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90123.7588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67915340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.357159
X-RAY DIFFRACTIONr_chiral_restr0.0690.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021778
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.2990
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21605
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.51523
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9622375
X-RAY DIFFRACTIONr_scbond_it1.1733964
X-RAY DIFFRACTIONr_scangle_it1.9854.5868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 67 -
Rwork0.259 1505 -
obs--96.68 %

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