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- PDB-4pbw: Crystal structure of chicken receptor protein tyrosine phosphatas... -

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Basic information

Entry
Database: PDB / ID: 4pbw
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 / Receptor protein tyrosine phosphatase (RPTP) / 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 / neurotrophin receptor activity / negative regulation of axon regeneration / neurotrophin binding / negative regulation of dendritic spine development / synaptic membrane adhesion / Activated NTRK3 signals through PI3K ...Receptor-type tyrosine-protein phosphatases / NTF3 activates NTRK3 signaling / Activated NTRK3 signals through PLCG1 / negative regulation of collateral sprouting / neurotrophin receptor activity / negative regulation of axon regeneration / neurotrophin binding / negative regulation of dendritic spine development / synaptic membrane adhesion / Activated NTRK3 signals through PI3K / negative regulation of axon extension / heparan sulfate proteoglycan binding / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / peptidyl-tyrosine dephosphorylation / transmembrane receptor protein tyrosine kinase activity / protein-tyrosine-phosphatase / cellular response to nerve growth factor stimulus / protein tyrosine phosphatase activity / postsynaptic density membrane / receptor protein-tyrosine kinase / synaptic vesicle membrane / positive regulation of neuron projection development / cell surface receptor protein tyrosine kinase signaling pathway / heparin binding / nervous system development / heart development / growth cone / perikaryon / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / axon / phosphorylation / 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 / Immunoglobulin domain ...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 / Leucine rich repeat / 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. / Leucine-rich repeat profile. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Leucine-rich repeat / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Leucine-rich repeat domain superfamily / Fibronectin type III / Fibronectin type III 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
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: 3.05 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
Revision 1.3Jul 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 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)194,0517
Polymers193,8306
Non-polymers2211
Water0
1
B: NT-3 growth factor receptor
E: Protein-tyrosine phosphatase CRYPalpha1 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8313
Polymers64,6102
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint0 kcal/mol
Surface area22320 Å2
MethodPISA
2
A: NT-3 growth factor receptor
D: Protein-tyrosine phosphatase CRYPalpha1 isoform


Theoretical massNumber of molelcules
Total (without water)64,6102
Polymers64,6102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-5 kcal/mol
Surface area22110 Å2
MethodPISA
3
C: NT-3 growth factor receptor
F: Protein-tyrosine phosphatase CRYPalpha1 isoform


Theoretical massNumber of molelcules
Total (without water)64,6102
Polymers64,6102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-2 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.420, 93.120, 99.380
Angle α, β, γ (deg.)73.37, 89.45, 74.23
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13A
23C
14D
24E
15D
25F
16E
26F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYVALVALBA31 - 3013 - 273
21GLYGLYVALVALAB31 - 3013 - 273
12GLYGLYTYRTYRBA31 - 3023 - 274
22GLYGLYTYRTYRCC31 - 3023 - 274
13GLYGLYTYRTYRAB31 - 3023 - 274
23GLYGLYTYRTYRCC31 - 3023 - 274
14GLUGLUARGARGDD29 - 2254 - 200
24GLUGLUARGARGEE29 - 2254 - 200
15GLUGLUVALVALDD29 - 2244 - 199
25GLUGLUVALVALFF29 - 2244 - 199
16GLUGLUVALVALEE29 - 2244 - 199
26GLUGLUVALVALFF29 - 2244 - 199

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 31888.920 Da / Num. of mol.: 3 / Mutation: yes
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: 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
Source method: isolated from a genetically manipulated source
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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% w/v PEG MME 5k, 0.1 M HEPES pH 7, 5% w/v Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.05→81.02 Å / Num. obs: 51063 / % possible obs: 96.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.8
Reflection shellResolution: 3.05→3.13 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 1.5 / % possible all: 96.6

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Processing

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

2yd4


Resolution: 3.05→94.96 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.915 / SU B: 46.384 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 0.95 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23994 2533 5 %RANDOM
Rwork0.2261 ---
obs0.22682 48530 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 115.246 Å2
Baniso -1Baniso -2Baniso -3
1--5.06 Å22.72 Å22.24 Å2
2--0.86 Å2-5.08 Å2
3---1.37 Å2
Refinement stepCycle: 1 / Resolution: 3.05→94.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10630 0 14 0 10644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01910867
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210300
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.94914797
X-RAY DIFFRACTIONr_angle_other_deg0.769323662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6851347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55224.922514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.676151827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7541575
X-RAY DIFFRACTIONr_chiral_restr0.0620.21713
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112349
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022464
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_it1.9136.1975424
X-RAY DIFFRACTIONr_mcbond_other1.9136.1975423
X-RAY DIFFRACTIONr_mcangle_it3.2069.2936759
X-RAY DIFFRACTIONr_mcangle_other3.2069.2936760
X-RAY DIFFRACTIONr_scbond_it2.2316.4475443
X-RAY DIFFRACTIONr_scbond_other2.236.4475444
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7739.5848039
X-RAY DIFFRACTIONr_long_range_B_refined5.66348.18611184
X-RAY DIFFRACTIONr_long_range_B_other5.66348.18611185
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)
11B159210.06
12A159210.06
21B155740.05
22C155740.05
31A155380.05
32C155380.05
41D111540.03
42E111540.03
51D111140.03
52F111140.03
61E111110.04
62F111110.04
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 167 -
Rwork0.372 3656 -
obs--96.49 %
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)
14.3274-0.4931-0.6183.17780.21952.20260.06440.56730.4753-0.44710.00950.1054-0.1005-0.0844-0.07390.2776-0.0059-0.03360.07980.09680.535732.7824-48.00764.6422
24.7625-0.24950.52052.1922-0.11252.19230.00050.41290.1085-0.19030.0488-0.09910.0527-0.0483-0.04940.1677-0.03120.13510.0467-0.02050.201313.200311.850865.7959
34.613-0.74990.11752.4529-0.02323.0282-0.171-0.23750.8692-0.30710.1181-0.5017-0.17040.71840.05290.62970.13810.05321.063-0.36410.485518.42346.210744.2762
42.7303-0.85910.36983.1751.1823.85430.0465-0.5185-0.29360.3297-0.156-0.07950.5059-0.25760.10950.2533-0.0492-0.00380.14560.03190.192317.2717-0.102886.5773
54.52090.0317-0.42724.0153-0.1972.98110.1269-0.84320.11181.1850.0906-0.1233-0.00040.1945-0.21750.48560.00630.03390.1645-0.03080.727226.8325-37.842285.9778
62.5306-0.8589-0.98190.77771.49324.2374-0.2284-0.4606-0.77490.4140.00370.38050.9221-0.24250.22470.77530.08330.00470.845-0.19560.53499.5604-14.351134.1645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B31 - 401
2X-RAY DIFFRACTION2A30 - 302
3X-RAY DIFFRACTION3C31 - 302
4X-RAY DIFFRACTION4D29 - 226
5X-RAY DIFFRACTION5E29 - 227
6X-RAY DIFFRACTION6F29 - 225

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