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- PDB-4pbx: Crystal structure of the six N-terminal domains of human receptor... -

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Basic information

Entry
Database: PDB / ID: 4pbx
TitleCrystal structure of the six N-terminal domains of human receptor protein tyrosine phosphatase sigma
ComponentsReceptor-type tyrosine-protein phosphatase S
KeywordsHYDROLASE / Signaling protein / Synapse Cell signalling Cell surface receptor
Function / homology
Function and homology information


negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / chondroitin sulfate binding / Receptor-type tyrosine-protein phosphatases / negative regulation of collateral sprouting / negative regulation of axon regeneration / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development ...negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / chondroitin sulfate binding / Receptor-type tyrosine-protein phosphatases / negative regulation of collateral sprouting / negative regulation of axon regeneration / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of axon extension / Synaptic adhesion-like molecules / corpus callosum development / negative regulation of interferon-beta production / heparan sulfate proteoglycan binding / spinal cord development / phosphoprotein phosphatase activity / peptidyl-tyrosine dephosphorylation / ECM proteoglycans / protein dephosphorylation / cerebellum development / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / hippocampus development / postsynaptic density membrane / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / cerebral cortex development / synaptic vesicle membrane / negative regulation of neuron projection development / presynaptic membrane / heparin binding / growth cone / perikaryon / receptor complex / axon / glutamatergic synapse / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsColes, C.H. / Mitakidis, N. / Zhang, P. / Elegheert, J. / Lu, W. / Stoker, A.W. / Nakagawa, T. / Craig, A.M. / Jones, E.Y. / Aricescu, A.R.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0700232 United Kingdom
Medical Research Council (United Kingdom)G9900061 United Kingdom
Cancer Research UKA10976 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
Wellcome TrustDPhil Studentship for N.M. United Kingdom
CitationJournal: Nat Commun / Year: 2014
Title: Structural basis for extracellular cis and trans RPTP sigma signal competition in synaptogenesis.
Authors: Coles, C.H. / Mitakidis, N. / Zhang, P. / Elegheert, J. / Lu, W. / Stoker, A.W. / Nakagawa, T. / Craig, A.M. / Jones, E.Y. / Aricescu, A.R.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_sheet_hbond ...pdbx_audit_support / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _pdbx_audit_support.funding_organization / _struct_sheet.number_strands
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Receptor-type tyrosine-protein phosphatase S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7863
Polymers64,3441
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint7 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.780, 198.780, 132.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase S / R-PTP-S / Receptor-type tyrosine-protein phosphatase sigma / R-PTP-sigma


Mass: 64344.035 Da / Num. of mol.: 1 / Fragment: Residues 30-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRS / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13332, protein-tyrosine-phosphatase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Compound detailsThe sample sequence matches to isoform 6 of UniProt Q13332

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.87 Å3/Da / Density % sol: 79.04 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10 % PEG 400, 0.01 M magnesium chloride, 0.1 M potassium chloride, 0.05 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.15→99.4 Å / Num. obs: 25619 / % possible obs: 95.6 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.8
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 2.1 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YD3, 2YD4, 2YD9, 2DJU

2yd3

2yd4

2yd9

2dju


Resolution: 3.15→172.15 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.9 / SU B: 42.451 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26497 1309 5.1 %RANDOM
Rwork0.23406 ---
obs0.23562 24310 94.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 120.828 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å2-0 Å2
2--0.7 Å2-0 Å2
3----2.28 Å2
Refinement stepCycle: 1 / Resolution: 3.15→172.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 28 0 4408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194510
X-RAY DIFFRACTIONr_bond_other_d0.0010.024227
X-RAY DIFFRACTIONr_angle_refined_deg1.0081.976145
X-RAY DIFFRACTIONr_angle_other_deg0.66739762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9455567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67824.308195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84315735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6751533
X-RAY DIFFRACTIONr_chiral_restr0.060.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02961
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6576.0442271
X-RAY DIFFRACTIONr_mcbond_other1.6586.0442270
X-RAY DIFFRACTIONr_mcangle_it2.9099.0652837
X-RAY DIFFRACTIONr_mcangle_other2.9099.0652838
X-RAY DIFFRACTIONr_scbond_it1.3956.1572238
X-RAY DIFFRACTIONr_scbond_other1.3956.1572238
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5259.183308
X-RAY DIFFRACTIONr_long_range_B_refined4.51546.4774655
X-RAY DIFFRACTIONr_long_range_B_other4.51546.4764655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 103 -
Rwork0.371 1755 -
obs--94.89 %
Refinement TLS params.Method: refined / Origin x: 38.1702 Å / Origin y: 60.3787 Å / Origin z: -30.8847 Å
111213212223313233
T0.4833 Å20.0295 Å20.0798 Å2-0.8713 Å2-0.023 Å2--0.2999 Å2
L3.1688 °2-1.04 °2-1.3555 °2-0.6741 °20.4551 °2--0.5899 °2
S-0.4109 Å °-1.0887 Å °-0.6658 Å °0.2066 Å °0.1649 Å °0.2342 Å °0.1954 Å °0.5149 Å °0.246 Å °

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