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- PDB-5wy8: Crystal structure of PTP delta Ig1-Ig3 in complex with IL1RAPL1 I... -

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Basic information

Entry
Database: PDB / ID: 5wy8
TitleCrystal structure of PTP delta Ig1-Ig3 in complex with IL1RAPL1 Ig1-Ig3
Components
  • Interleukin-1 receptor accessory protein-like 1
  • Receptor-type tyrosine-protein phosphatase delta
KeywordsHYDROLASE/PROTEIN BINDING / Synaptic adhesion / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Interleukin-38 signaling / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / Synaptic adhesion-like molecules ...trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Interleukin-38 signaling / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / Synaptic adhesion-like molecules / negative regulation of receptor signaling pathway via JAK-STAT / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / phosphate-containing compound metabolic process / negative regulation of exocytosis / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / regulation of postsynapse organization / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of presynapse assembly / regulation of immune response / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / neuron differentiation / presynaptic membrane / postsynaptic membrane / receptor complex / axon / signaling receptor binding / glutamatergic synapse / dendrite / cell surface / signal transduction / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / 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 delta / Interleukin-1 receptor accessory protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsKim, H.M. / Won, S.Y. / Kim, D.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
NRFNRF-2015R1A2A2A01005533 Korea, Republic Of
CitationJournal: Front Mol Neurosci / Year: 2017
Title: LAR-RPTP Clustering Is Modulated by Competitive Binding between Synaptic Adhesion Partners and Heparan Sulfate
Authors: Won, S.Y. / Kim, C.Y. / Kim, D. / Ko, J. / Um, J.W. / Lee, S.B. / Buck, M. / Kim, E. / Heo, W.D. / Lee, J.O. / Kim, H.M.
History
DepositionJan 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / 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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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: Interleukin-1 receptor accessory protein-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,76812
Polymers69,7402
Non-polymers3,02810
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint8 kcal/mol
Surface area33680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.416, 110.416, 210.536
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-1201-

HOH

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 32729.963 Da / Num. of mol.: 1 / Fragment: UNP residues 21-318
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 Interleukin-1 receptor accessory protein-like 1 / IL1RAPL-1 / Oligophrenin-4 / Three immunoglobulin domain-containing IL-1 receptor-related 2 / ...IL1RAPL-1 / Oligophrenin-4 / Three immunoglobulin domain-containing IL-1 receptor-related 2 / TIGIRR-2 / X-linked interleukin-1 receptor accessory protein-like 1


Mass: 37009.973 Da / Num. of mol.: 1 / Fragment: UNP residues 27-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RAPL1, OPHN4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NZN1

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Sugars , 4 types, 7 molecules

#3: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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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Non-polymers , 2 types, 9 molecules

#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 5.31 Å3/Da / Density % sol: 76.85 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 100mM Tris-Cl, PH7.5, 200mM zinc acetate, 10% PEG 8000(v/v)

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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: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 28613 / % possible obs: 97.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 88.06 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.774 / Net I/σ(I): 11.7 / Num. measured all: 223878
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3-3.116.50.57126921.173193.8
3.11-3.236.90.43827721.284194.8
3.23-3.387.50.32327971.37197.3
3.38-3.567.80.23928561.536198.3
3.56-3.787.90.17528511.648198.5
3.78-4.077.70.11829041.808199.2
4.07-4.487.90.07628912.018199.6
4.48-5.138.20.06429152.126199.5
5.13-6.4690.06129482.087199.8
6.46-508.70.04829872.255197.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→48.892 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 1992 7.22 %Random selection
Rwork0.2325 25583 --
obs0.2341 27575 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.66 Å2 / Biso mean: 91.2701 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.07→48.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4886 0 189 6 5081
Biso mean--102.99 66.03 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065192
X-RAY DIFFRACTIONf_angle_d0.9767066
X-RAY DIFFRACTIONf_chiral_restr0.062820
X-RAY DIFFRACTIONf_plane_restr0.007897
X-RAY DIFFRACTIONf_dihedral_angle_d19.0863160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0698-3.14660.31391380.32451748188696
3.1466-3.23160.3441370.308518121949100
3.2316-3.32670.30781410.284218341975100
3.3267-3.4340.31461420.284818221964100
3.434-3.55670.28861450.273218311976100
3.5567-3.69910.29021350.25718241959100
3.6991-3.86740.26911450.24418081953100
3.8674-4.07120.24441440.229418461990100
4.0712-4.32610.24081390.207518301969100
4.3261-4.65990.2231500.182718401990100
4.6599-5.12840.20121460.191618301976100
5.1284-5.86940.22791460.214218612007100
5.8694-7.39070.2591490.235918732022100
7.3907-48.89830.26271350.24321824195995

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