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- PDB-2iep: Crystal structure of immunoglobulin-like domains 1 and 2 of the r... -

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Basic information

Entry
Database: PDB / ID: 2iep
TitleCrystal structure of immunoglobulin-like domains 1 and 2 of the receptor tyrosine kinase MuSK
ComponentsMuscle-specific kinase receptor
KeywordsSIGNALING PROTEIN / TRANSFERASE / beta-sandwich
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 / 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 / protein tyrosine kinase activity / postsynaptic membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / receptor complex / positive regulation of protein 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 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 / Immunoglobulin-like domain superfamily / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / Mainly 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: 2.205 Å
AuthorsStiegler, A.L. / Burden, S.J. / Hubbard, S.R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the Agrin-responsive Immunoglobulin-like Domains 1 and 2 of the Receptor Tyrosine Kinase MuSK
Authors: Stiegler, A.L. / Burden, S.J. / Hubbard, S.R.
History
DepositionSep 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muscle-specific kinase receptor
B: Muscle-specific kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1835
Polymers41,8942
Non-polymers2883
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Muscle-specific kinase receptor
hetero molecules

A: Muscle-specific kinase receptor
hetero molecules

A: Muscle-specific kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2267
Polymers62,8423
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_654-x+1,-y,z-11
Buried area6090 Å2
ΔGint-111 kcal/mol
Surface area38170 Å2
MethodPISA
3
A: Muscle-specific kinase receptor
B: Muscle-specific kinase receptor
hetero molecules

A: Muscle-specific kinase receptor
B: Muscle-specific kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,36510
Polymers83,7894
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.608, 118.004, 57.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Muscle-specific kinase receptor / E.C.2.7.10.1 / Muscle / skeletal receptor tyrosine protein kinase / MuSK


Mass: 20947.211 Da / Num. of mol.: 2 / Fragment: Ectodomain Ig1-2 (residues 22-212)
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8% PEG 4000, 0.2M Ammonium Sulfate, 0.1M Sodium Acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.92014 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92014 Å / Relative weight: 1
ReflectionResolution: 2.205→50 Å / Num. obs: 27127 / % possible obs: 98.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Χ2: 1.311 / Net I/σ(I): 15.9
Reflection shellResolution: 2.205→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.331 / Num. unique all: 2620 / Χ2: 1.631 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FHG

1fhg


Resolution: 2.205→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.172 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1309 5 %RANDOM
Rwork0.216 ---
obs0.218 26130 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2---0.99 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.205→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 15 175 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222892
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9913932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23725104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83515517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3921516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022084
X-RAY DIFFRACTIONr_nbd_refined0.1920.21097
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.224
X-RAY DIFFRACTIONr_mcbond_it0.7541.51924
X-RAY DIFFRACTIONr_mcangle_it1.23323032
X-RAY DIFFRACTIONr_scbond_it1.73431095
X-RAY DIFFRACTIONr_scangle_it2.8964.5900
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 85 -
Rwork0.225 1631 -
obs-1716 86.4 %

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