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- PDB-4yfd: Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP -

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Basic information

Entry
Database: PDB / ID: 4yfd
TitleCrystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP
Components
  • Interleukin-1 receptor accessory protein
  • Receptor-type tyrosine-protein phosphatase delta
KeywordsIMMUNE SYSTEM/HYDROLASE / trans-synaptic complex / synapse organizer / IMMUNE SYSTEM-HYDROLASE complex
Function / homology
Function and homology information


Interleukin-33 signaling / Interleukin-36 pathway / interleukin-33 receptor activity / trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / interleukin-1 receptor activity / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / Interleukin-1 signaling ...Interleukin-33 signaling / Interleukin-36 pathway / interleukin-33 receptor activity / trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / interleukin-1 receptor activity / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / Interleukin-1 signaling / PIP3 activates AKT signaling / synaptic membrane adhesion / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / interleukin-33-mediated signaling pathway / positive regulation of dendritic spine morphogenesis / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / regulation of postsynaptic density assembly / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of dendrite morphogenesis / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / interleukin-1-mediated signaling pathway / positive regulation of interleukin-4 production / regulation of presynapse assembly / regulation of immune response / coreceptor activity / cell adhesion molecule binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein tyrosine kinase binding / hippocampal mossy fiber to CA3 synapse / positive regulation of NF-kappaB transcription factor activity / modulation of chemical synaptic transmission / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / inflammatory response / signaling receptor binding / innate immune response / synapse / glutamatergic synapse / extracellular region / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / : / TIR domain / Immunoglobulin domain / Toll - interleukin 1 - resistance / TIR domain profile. ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / : / TIR domain / Immunoglobulin domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / 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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-1 receptor accessory protein / Receptor-type tyrosine-protein phosphatase delta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.253 Å
AuthorsYamagata, A. / Fukai, S.
CitationJournal: Nat Commun / Year: 2015
Title: Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Authors: Yamagata, A. / Yoshida, T. / Sato, Y. / Goto-Ito, S. / Uemura, T. / Maeda, A. / Shiroshima, T. / Iwasawa-Okamoto, S. / Mori, H. / Mishina, M. / Fukai, S.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site ..._chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Interleukin-1 receptor accessory protein
A: Receptor-type tyrosine-protein phosphatase delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8299
Polymers93,2812
Non-polymers1,5487
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint12 kcal/mol
Surface area43360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.497, 63.306, 169.350
Angle α, β, γ (deg.)90.00, 94.23, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Interleukin-1 receptor accessory protein / IL-1RAcP


Mass: 39368.535 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il1rap / Cell line (production host): Freestyle 293-F / Production host: Homo sapiens (human) / References: UniProt: Q61730
#2: Protein Receptor-type tyrosine-protein phosphatase delta / R-PTP-delta


Mass: 53912.441 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Cell line (production host): Freestyle 293-F / Production host: Homo sapiens (human) / References: UniProt: Q64487, protein-tyrosine-phosphatase
#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.: 7
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
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: 4.34 Å3/Da / Density % sol: 71.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% PEG3350, 0.1 M ammonium sulfate and 0.1 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 25436 / % possible obs: 97.3 % / Redundancy: 4.7 % / Rsym value: 0.118 / Net I/σ(I): 10.7
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YD6, 2YD9, 4DEP, 3O4O, 4YFE

2yd6

2yd9

4dep

3o4o

4yfe


Resolution: 3.253→48.974 Å / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 33.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2867 1292 5.08 %
Rwork0.2558 --
obs0.2574 25418 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.253→48.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6505 0 0 0 6505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056676
X-RAY DIFFRACTIONf_angle_d1.1499104
X-RAY DIFFRACTIONf_dihedral_angle_d17.1312485
X-RAY DIFFRACTIONf_chiral_restr0.0481037
X-RAY DIFFRACTIONf_plane_restr0.0061186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2525-3.38270.41681120.38722540X-RAY DIFFRACTION92
3.3827-3.53660.37131532597X-RAY DIFFRACTION94
3.5366-3.7230.3861370.32392581X-RAY DIFFRACTION95
3.723-3.95620.29981430.28522653X-RAY DIFFRACTION97
3.9562-4.26150.28231420.23372678X-RAY DIFFRACTION98
4.2615-4.690.24151460.20352707X-RAY DIFFRACTION99
4.69-5.3680.22761370.18932759X-RAY DIFFRACTION99
5.368-6.76020.27051580.24762765X-RAY DIFFRACTION99
6.7602-48.97920.26441640.23932846X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.6804 Å / Origin y: 14.5936 Å / Origin z: 31.1471 Å
111213212223313233
T0.5213 Å2-0.1218 Å2-0.0017 Å2-0.2613 Å2-0.0353 Å2--0.5726 Å2
L0.9261 °2-0.2226 °2-0.2828 °2-0.2729 °20.3176 °2--0.1207 °2
S0.0439 Å °0.0365 Å °-0.1008 Å °-0.0589 Å °0.108 Å °-0.0725 Å °-0.2196 Å °0.0344 Å °-0.127 Å °
Refinement TLS groupSelection details: all

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