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- PDB-7ceg: Crystal structure of the complex between mouse PTP delta and neur... -

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Basic information

Entry
Database: PDB / ID: 7ceg
TitleCrystal structure of the complex between mouse PTP delta and neuroligin-3
Components
  • Isoform C of Receptor-type tyrosine-protein phosphatase delta
  • Neuroligin-3
KeywordsHYDROLASE/CELL ADHESION / synapse organization / trans-synaptic complex / esterase domain / HYDROLASE-CELL ADHESION complex
Function / homology
Function and homology information


negative regulation of dendritic spine morphogenesis / positive regulation of AMPA receptor activity / rhythmic synaptic transmission / trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / Neurexins and neuroligins / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / regulation of terminal button organization / positive regulation of synaptic vesicle clustering ...negative regulation of dendritic spine morphogenesis / positive regulation of AMPA receptor activity / rhythmic synaptic transmission / trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / Neurexins and neuroligins / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / regulation of terminal button organization / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly / presynaptic membrane assembly / neurexin family protein binding / synaptic membrane adhesion / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / negative regulation of excitatory postsynaptic potential / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / positive regulation of glutamate receptor signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of dendrite morphogenesis / regulation of AMPA receptor activity / regulation of dendritic spine morphogenesis / regulation of NMDA receptor activity / axon extension / regulation of long-term synaptic potentiation / positive regulation of synapse assembly / heterophilic cell-cell adhesion / inhibitory postsynaptic potential / oligodendrocyte differentiation / excitatory synapse / social behavior / endocytic vesicle / positive regulation of excitatory postsynaptic potential / regulation of immune response / positive regulation of synaptic transmission, glutamatergic / regulation of synaptic transmission, glutamatergic / cell adhesion molecule binding / protein-tyrosine-phosphatase / receptor-mediated endocytosis / protein tyrosine phosphatase activity / hippocampal mossy fiber to CA3 synapse / excitatory postsynaptic potential / synapse organization / visual learning / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / long-term synaptic potentiation / neuron differentiation / presynaptic membrane / postsynaptic membrane / signaling receptor binding / synapse / glutamatergic synapse / cell surface
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Neuroligin / : / : / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Neuroligin / : / : / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / 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 profile. / Tyrosine-specific protein phosphatases domain / 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 / Alpha/Beta hydrolase fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase delta / Neuroligin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å
AuthorsYamagata, A. / Yoshida, T. / Shiroshima, T. / Maeda, A. / Fukai, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H04749 Japan
Japan Society for the Promotion of Science (JSPS)JP25293057 Japan
Japan Society for the Promotion of Science (JSPS)JP24247014 Japan
Japan Science and TechnologyJPMJCR12M5 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice.
Authors: Yoshida, T. / Yamagata, A. / Imai, A. / Kim, J. / Izumi, H. / Nakashima, S. / Shiroshima, T. / Maeda, A. / Iwasawa-Okamoto, S. / Azechi, K. / Osaka, F. / Saitoh, T. / Maenaka, K. / Shimada, ...Authors: Yoshida, T. / Yamagata, A. / Imai, A. / Kim, J. / Izumi, H. / Nakashima, S. / Shiroshima, T. / Maeda, A. / Iwasawa-Okamoto, S. / Azechi, K. / Osaka, F. / Saitoh, T. / Maenaka, K. / Shimada, T. / Fukata, Y. / Fukata, M. / Matsumoto, J. / Nishijo, H. / Takao, K. / Tanaka, S. / Okabe, S. / Tabuchi, K. / Uemura, T. / Mishina, M. / Mori, H. / Fukai, S.
History
DepositionJun 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform C of Receptor-type tyrosine-protein phosphatase delta
B: Neuroligin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7786
Polymers106,8932
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint2 kcal/mol
Surface area41630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.109, 96.109, 371.613
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

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


Mass: 42384.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q64487, protein-tyrosine-phosphatase
#2: Protein Neuroligin-3 / Gliotactin homolog


Mass: 64508.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: HEK293F / Gene: Nlgn3 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q8BYM5
#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.: 4
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 ligand of interestN
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: 4.28 Å3/Da / Density % sol: 71.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10% PEG 3350, 0.1 M ammonium iodide, 0.1 M MES-Na

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. obs: 19070 / % possible obs: 98.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 142.02 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.034 / Rrim(I) all: 0.124 / Χ2: 0.799 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.22-4.35.10.3397110.5820.1480.3730.37598.5
4.3-4.385.50.3437870.5690.1450.3740.3797.3
4.38-4.475.40.3227010.8940.1370.3520.41597.9
4.47-4.575.90.3097490.760.1230.3340.4598.4
4.57-4.675.50.2797190.8270.1140.3040.53797
4.67-4.797.10.2957720.9570.1070.3160.51997.7
4.79-4.927.50.2857200.8780.1010.3040.598.1
4.92-5.068.20.2817650.8850.0940.2980.48898.8
5.06-5.238.40.2567360.910.0860.2710.4898.8
5.23-5.418.40.2477550.9360.0830.2610.54798.4
5.41-5.638.70.2447550.9450.0790.2570.53698.6
5.63-5.898.40.2277370.9640.0750.240.53798.8
5.89-6.29.10.2157760.9650.0680.2260.5798.9
6.2-6.589.10.1957340.9780.0620.2060.60799.1
6.58-7.099.20.1687700.9820.0520.1770.77698.6
7.09-7.812.90.1447670.9920.0380.150.85999.1
7.8-8.9314.50.1187910.9940.0290.1221.05299.5
8.93-11.2216.80.0937830.9960.0220.0951.18299
11.22-5016.40.0888340.9980.0220.0911.77498.5

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YD6, 4YFD, 4YFE, 3BIX

2yd6

4yfd

4yfe

3bix


Resolution: 3.85→49.69 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2891 928 4.87 %
Rwork0.2531 --
obs0.2547 19070 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.85→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7273 0 0 0 7273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027470
X-RAY DIFFRACTIONf_angle_d0.49910200
X-RAY DIFFRACTIONf_dihedral_angle_d14.422740
X-RAY DIFFRACTIONf_chiral_restr0.0461135
X-RAY DIFFRACTIONf_plane_restr0.0041334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.85-4.050.37891320.31862485X-RAY DIFFRACTION98
4.05-4.30.30491550.27532542X-RAY DIFFRACTION100
4.3-4.630.30531390.24882576X-RAY DIFFRACTION100
4.63-5.10.28871190.24252593X-RAY DIFFRACTION100
5.1-5.840.28171200.25262595X-RAY DIFFRACTION100
5.84-7.350.31591400.2962635X-RAY DIFFRACTION100
7.35-49.690.2561230.22892716X-RAY DIFFRACTION100
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)
12.7112-0.1218-1.07785.13920.35161.2705-0.1654-0.80970.09720.81980.1281-0.01220.5338-0.41080.06771.79220.26560.20221.30630.03051.1924-3.182-26.448-20.5
22.28760.3371-0.35381.3621.02686.4564-0.5941-0.5359-0.515-0.20830.56690.11651.2575-0.89780.0522.55050.05530.29481.21730.29081.8362-3.206-32.453-44.551
36.21791.23524.6129.2998-3.93986.4971-0.34440.55420.5045-0.03350.1818-0.37670.3243-0.21230.12361.84610.8020.06891.5177-0.21261.5094-3.58418.028-26.087
44.462-3.94440.7995.876-1.29812.62420.47210.5006-0.1286-0.8657-0.46730.3437-0.00250.6643-0.08462.04050.43640.00361.2235-0.08071.489317.409-13.514-36.215
5-0.728-0.88631.30285.1268-5.08413.42830.1792-0.13170.95810.282-0.3916-0.1349-0.14070.09030.21472.32670.9961-0.18081.6662-0.15441.702343.42-61.586-2.804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 37:363 )B37 - 363
2X-RAY DIFFRACTION2( CHAIN B AND RESID 364:615 )B364 - 615
3X-RAY DIFFRACTION3( CHAIN A AND RESID 28:137 )A28 - 137
4X-RAY DIFFRACTION4( CHAIN A AND RESID 138:302 )A138 - 302
5X-RAY DIFFRACTION5( CHAIN A AND RESID 303:413 )A303 - 413

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