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- PDB-4rca: Crystal structure of human PTPdelta and human Slitrk1 complex -

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Basic information

Entry
Database: PDB / ID: 4rca
TitleCrystal structure of human PTPdelta and human Slitrk1 complex
Components
  • Receptor-type tyrosine-protein phosphatase delta
  • SLIT and NTRK-like protein 1
KeywordsSIGNALING PROTEIN / Leucine rich-repeat / Ig-like domain / synaptic adhesion
Function / homology
Function and homology information


trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / presynapse assembly / vocalization behavior / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly ...trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / presynapse assembly / vocalization behavior / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / Synaptic adhesion-like molecules / negative regulation of receptor signaling pathway via JAK-STAT / norepinephrine metabolic process / phosphate-containing compound metabolic process / positive regulation of axonogenesis / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / neuron projection extension / homeostatic process / adult behavior / regulation of presynapse assembly / regulation of immune response / synapse assembly / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / axonogenesis / hippocampal mossy fiber to CA3 synapse / GABA-ergic synapse / modulation of chemical synaptic transmission / postsynaptic density membrane / Schaffer collateral - CA1 synapse / multicellular organism growth / endocytosis / neuron differentiation / presynaptic membrane / gene expression / cellular response to hypoxia / signaling receptor binding / synapse / glutamatergic synapse / signal transduction / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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 / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / 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 / 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 / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase delta / SLIT and NTRK-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9908 Å
AuthorsKim, H.M. / Park, B.S. / Kim, D. / Lee, S.G.
CitationJournal: Nat Commun / Year: 2014
Title: Structural basis for LAR-RPTP/Slitrk complex-mediated synaptic adhesion.
Authors: Um, J.W. / Kim, K.H. / Park, B.S. / Choi, Y. / Kim, D. / Kim, C.Y. / Kim, S.J. / Kim, M. / Ko, J.S. / Lee, S.G. / Choii, G. / Nam, J. / Heo, W.D. / Kim, E. / Lee, J.O. / Ko, J. / Kim, H.M.
History
DepositionSep 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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
Revision 1.5Nov 6, 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: Receptor-type tyrosine-protein phosphatase delta
B: SLIT and NTRK-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2786
Polymers62,5182
Non-polymers7604
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.981, 60.195, 83.679
Angle α, β, γ (deg.)90.00, 102.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33853.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRD / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23468, protein-tyrosine-phosphatase
#2: Protein SLIT and NTRK-like protein 1 / Leucine-rich repeat-containing protein 12


Mass: 28664.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLITRK1, KIAA1910, LRRC12, UNQ233/PRO266 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96PX8
#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.: 3
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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-Cl, pH 8.5, 200 mM ammonium sulfate, and 20% PEG3350 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 296.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.9908→50 Å / Num. all: 15343 / Num. obs: 15130 / % possible obs: 98.6 % / Observed criterion σ(I): 2.59 / Redundancy: 4.4 % / Biso Wilson estimate: 59.2 Å2 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.9908-3.05195.9
3.05-3.11195.6
3.11-3.17196.4
3.17-3.23197.6
3.23-3.3198.2
3.3-3.38199.1
3.38-3.46199.1
3.46-3.56199
3.56-3.66199.3
3.66-3.78199.2
3.78-3.91199.5
3.91-4.07199.4
4.07-4.26199.7
4.26-4.48199.6
4.48-4.76199.7
4.76-5.13199.5
5.13-5.64199.5
5.64-6.46199.7
6.46-8.13199.9
8.13-50196.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RCW, 2YD6

4rcw

2yd6


Resolution: 2.9908→38.615 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.884 / SU ML: 0.46 / σ(F): 1.41 / Phase error: 30.71 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2691 758 5.02 %
Rwork0.2625 --
obs0.2628 15094 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.937 Å2
Baniso -1Baniso -2Baniso -3
1-12.41 Å20 Å22.02 Å2
2---3.79 Å20 Å2
3----8.29 Å2
Refinement stepCycle: LAST / Resolution: 2.9908→38.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 47 2 4287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164378
X-RAY DIFFRACTIONf_angle_d0.8465939
X-RAY DIFFRACTIONf_dihedral_angle_d15.0451648
X-RAY DIFFRACTIONf_chiral_restr0.044681
X-RAY DIFFRACTIONf_plane_restr0.003782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9908-3.22160.36981330.38482736X-RAY DIFFRACTION94
3.2216-3.54560.34071470.30832854X-RAY DIFFRACTION99
3.5456-4.05820.26941630.26012891X-RAY DIFFRACTION99
4.0582-5.1110.22711600.22462901X-RAY DIFFRACTION100
5.111-38.61770.24031550.22832954X-RAY DIFFRACTION99

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