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Basic information

Entry
Database: PDB / ID: 4pbv
TitleCrystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC
Components
  • NT-3 growth factor receptor
  • Protein-tyrosine phosphatase CRYPalpha1 isoform
KeywordsSIGNALING PROTEIN / Synapse Cell signalling Cell surface receptor
Function / homology
Function and homology information


Receptor-type tyrosine-protein phosphatases / NTF3 activates NTRK3 signaling / Activated NTRK3 signals through PLCG1 / negative regulation of collateral sprouting / negative regulation of axon regeneration / neurotrophin receptor activity / neurotrophin binding / negative regulation of dendritic spine development / synaptic membrane adhesion / negative regulation of axon extension ...Receptor-type tyrosine-protein phosphatases / NTF3 activates NTRK3 signaling / Activated NTRK3 signals through PLCG1 / negative regulation of collateral sprouting / negative regulation of axon regeneration / neurotrophin receptor activity / neurotrophin binding / negative regulation of dendritic spine development / synaptic membrane adhesion / negative regulation of axon extension / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / heparan sulfate proteoglycan binding / peptidyl-tyrosine dephosphorylation / protein-tyrosine-phosphatase / transmembrane receptor protein tyrosine kinase activity / protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of neuron projection development / receptor protein-tyrosine kinase / cellular response to nerve growth factor stimulus / postsynaptic density membrane / synaptic vesicle membrane / nervous system development / heparin binding / heart development / growth cone / perikaryon / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / axon / signal transduction / protein homodimerization activity / ATP binding / plasma membrane
Similarity search - Function
NT-3 growth factor receptor NTRK3 / : / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Immunoglobulin ...NT-3 growth factor receptor NTRK3 / : / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Leucine rich repeat / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Leucine-rich repeat profile. / Fibronectin type III domain / : / Fibronectin type 3 domain / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Leucine-rich repeat domain superfamily / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase S / Receptor-type tyrosine-protein phosphatase S / NT-3 growth factor receptor
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / 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 2.2Dec 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NT-3 growth factor receptor
B: NT-3 growth factor receptor
C: Protein-tyrosine phosphatase CRYPalpha1 isoform
D: Protein-tyrosine phosphatase CRYPalpha1 isoform
E: Protein-tyrosine phosphatase CRYPalpha1 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,26012
Polymers158,9625
Non-polymers1,2987
Water2,126118
1
A: NT-3 growth factor receptor
C: Protein-tyrosine phosphatase CRYPalpha1 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7845
Polymers63,1202
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint3 kcal/mol
Surface area23300 Å2
MethodPISA
2
B: NT-3 growth factor receptor
D: Protein-tyrosine phosphatase CRYPalpha1 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6595
Polymers63,1202
Non-polymers5383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-10 kcal/mol
Surface area22780 Å2
MethodPISA
3
E: Protein-tyrosine phosphatase CRYPalpha1 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8172
Polymers32,7211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 122.160, 98.610
Angle α, β, γ (deg.)90.00, 109.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23E
14D
24E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTYRTYRAA31 - 3023 - 259
21GLYGLYTYRTYRBB31 - 3023 - 259
12GLUGLUVALVALCC29 - 2264 - 201
22GLUGLUVALVALDD29 - 2264 - 201
13GLUGLUARGARGCC29 - 2274 - 202
23GLUGLUARGARGEE29 - 2274 - 202
14GLUGLUVALVALDD29 - 2264 - 201
24GLUGLUVALVALEE29 - 2264 - 201

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein NT-3 growth factor receptor / Neurotrophic tyrosine kinase receptor type 3 / TrkC tyrosine kinase / Trk-C


Mass: 30399.387 Da / Num. of mol.: 2 / Fragment: Residues 31-302 / Mutation: N163Q, N232Q, N259Q, N267Q and N294Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: NTRK3, TRKC / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human)
References: UniProt: Q91044, receptor protein-tyrosine kinase
#2: Protein Protein-tyrosine phosphatase CRYPalpha1 isoform


Mass: 32721.014 Da / Num. of mol.: 3 / Fragment: Residues 29-316
Source method: isolated from a genetically manipulated source
Details: Ig3 domain is not visible in electron density, suggesting that this domain had either been proteolytically cleaved during crystallisation or is disordered.
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CRYPalpha1 / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q90815, UniProt: F1NWE3*PLUS
#3: 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.: 5 / 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% PEG 20k, 20% PEG MME 550, 0.1M bicine/Tris pH8.5, 0.03M sodium nitrate, 0.03M disodium hydrogen phosphate, 0.03M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→92.79 Å / Num. obs: 52662 / % possible obs: 99.8 % / Redundancy: 11.6 % / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YD4

2yd4


Resolution: 2.5→92.79 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 20.34 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.405 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24701 2676 5.1 %RANDOM
Rwork0.20858 ---
obs0.21055 49976 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å2-0 Å2-0.38 Å2
2---0.05 Å20 Å2
3---1.55 Å2
Refinement stepCycle: 1 / Resolution: 2.5→92.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8536 0 80 118 8734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198797
X-RAY DIFFRACTIONr_bond_other_d0.0010.028347
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.96811977
X-RAY DIFFRACTIONr_angle_other_deg0.7153.00319141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11651085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60324.746413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.794151469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.631565
X-RAY DIFFRACTIONr_chiral_restr0.0690.21373
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110004
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021965
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_it1.3783.4334370
X-RAY DIFFRACTIONr_mcbond_other1.3783.4334369
X-RAY DIFFRACTIONr_mcangle_it2.2725.1425445
X-RAY DIFFRACTIONr_mcangle_other2.2725.1425446
X-RAY DIFFRACTIONr_scbond_it1.8113.7084427
X-RAY DIFFRACTIONr_scbond_other1.8073.6994420
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9245.4626521
X-RAY DIFFRACTIONr_long_range_B_refined4.56826.7288760
X-RAY DIFFRACTIONr_long_range_B_other4.52826.6968746
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A14330.07
12B14330.07
21C10240.09
22D10240.09
31C10220.09
32E10220.09
41D10160.08
42E10160.08
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 184 -
Rwork0.322 3649 -
obs--99.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.07581.088-0.56371.9072-0.49261.5208-0.07520.2845-0.1407-0.1863-0.03390.01810.0980.09750.10910.08830.0163-0.06450.1835-0.02890.0808-13.229718.0775-64.0334
22.63381.1182-0.18071.9324-0.97671.6378-0.10860.2242-0.21780.02230.09560.0089-0.03220.03970.01310.03180.0003-0.00980.0694-0.0690.0966-0.439919.69-45.4111
31.28430.2620.29150.5339-0.01422.851-0.07780.23940.3979-0.06650.08790.1344-0.2274-0.0803-0.01020.2253-0.0365-0.0790.23850.08530.1915-25.074335.0294-76.8661
41.68560.48020.56611.9339-0.40992.59130.0097-0.1344-0.06540.3132-0.01670.3498-0.21530.05580.0070.08580.00410.02320.0236-0.00170.1442-10.258328.9472-24.7469
52.5692-0.08230.29293.9244-0.67451.6454-0.0286-0.38820.3870.62850.03410.2201-0.1928-0.3085-0.00550.12410.0074-0.02350.1406-0.00910.2455-45.552846.3862-30.1707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 304
2X-RAY DIFFRACTION2B31 - 303
3X-RAY DIFFRACTION3C29 - 227
4X-RAY DIFFRACTION4D29 - 226
5X-RAY DIFFRACTION5E29 - 228

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