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- PDB-6kip: Crystal structure of PTPRD phosphatase domain in complex with Lip... -

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Basic information

Entry
Database: PDB / ID: 6kip
TitleCrystal structure of PTPRD phosphatase domain in complex with Liprin-alpha3 tandem SAM domains
Components
  • Liprin-alpha-3
  • Receptor-type tyrosine-protein phosphatase delta
KeywordsHYDROLASE/PROTEIN BINDING / Synapse / Protein tyrosine phosphatase / SAM / PROTEIN BINDING / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


epididymosome / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex ...epididymosome / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / synaptic vesicle docking / regulation of postsynaptic density assembly / synaptic membrane adhesion / presynaptic active zone cytoplasmic component / negative regulation of receptor signaling pathway via JAK-STAT / neurotransmitter secretion / regulation of short-term neuronal synaptic plasticity / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / presynaptic active zone / synaptic vesicle exocytosis / regulation of immune response / dephosphorylation / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / protein-tyrosine-phosphatase / acrosomal vesicle / protein tyrosine phosphatase activity / synapse organization / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / neuron differentiation / presynaptic membrane / receptor complex / signaling receptor binding / glutamatergic synapse / synapse / cytoplasm
Similarity search - Function
Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / LAR-interacting protein, Liprin / Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / Protein tyrosine phosphatase superfamily / Immunoglobulin domain ...Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / LAR-interacting protein, Liprin / Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / Protein tyrosine phosphatase superfamily / Immunoglobulin domain / Protein-Tyrosine Phosphatase; Chain A / SAM domain profile. / Sterile alpha motif. / Protein tyrosine phosphatase, catalytic domain / Sterile alpha motif 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 / Sterile alpha motif/pointed domain superfamily / 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 / DNA polymerase; domain 1 / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Liprin-alpha-3 / Receptor-type tyrosine-protein phosphatase delta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.911 Å
AuthorsWakita, M. / Yamagata, A. / Fukai, S.
CitationJournal: Nat Commun / Year: 2020
Title: Structural insights into selective interaction between type IIa receptor protein tyrosine phosphatases and Liprin-alpha.
Authors: Wakita, M. / Yamagata, A. / Shiroshima, T. / Izumi, H. / Maeda, A. / Sendo, M. / Imai, A. / Kubota, K. / Goto-Ito, S. / Sato, Y. / Mori, H. / Yoshida, T. / Fukai, S.
History
DepositionJul 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase delta
B: Liprin-alpha-3


Theoretical massNumber of molelcules
Total (without water)73,0932
Polymers73,0932
Non-polymers00
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-8 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.012, 98.012, 140.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-1202-

HOH

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Components

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


Mass: 35552.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q64487, protein-tyrosine-phosphatase
#2: Protein Liprin-alpha-3 / Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-3 / PTPRF- ...Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-3 / PTPRF-interacting protein alpha-3


Mass: 37540.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppfia3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P60469
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 15% PEG 3350 and 0.1 M Tris-HCl (pH 8.5)

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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 EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 52100 / % possible obs: 97.3 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.026 / Rrim(I) all: 0.108 / Χ2: 1.489 / Net I/σ(I): 7.4 / Num. measured all: 530555
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.91-1.943.50.27824040.5950.1490.3180.40191.2
1.94-1.9840.27624330.630.1390.3120.42293.1
1.98-2.024.20.25224570.7560.1230.2830.43693.4
2.02-2.064.70.24225090.8150.110.2680.47295.3
2.06-2.15.30.23125240.890.0950.2510.54696.4
2.1-2.155.80.2225630.9210.0870.2380.61196.5
2.15-2.26.40.20625360.9440.0760.220.65797.2
2.2-2.266.70.19726030.9550.070.210.73897.2
2.26-2.3370.18325690.9680.0640.1950.86497.2
2.33-2.4180.17725980.9720.0570.1860.85798
2.41-2.498.60.16725800.980.0520.1761.00797.9
2.49-2.59100.15926290.9880.0450.1651.03298.5
2.59-2.7110.90.14826270.9880.0410.1541.09398.6
2.71-2.85120.14126380.990.0380.1471.29198.9
2.85-3.0312.20.13126620.9910.0340.1351.40699.1
3.03-3.2714.20.1226690.9930.0290.1241.63799.1
3.27-3.5917.50.10826970.9950.0240.111.85699.8
3.59-4.11190.09627120.9960.0210.0982.00199.6
4.11-5.1819.70.09227640.9970.020.0942.26699.7
5.18-5019.70.08829260.9960.020.0912.37699.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FH7, 3TAD

2fh7

3tad


Resolution: 1.911→49.25 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 18.41
RfactorNum. reflection% reflection
Rfree0.2084 2583 4.96 %
Rwork0.1622 --
obs0.1645 52074 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.89 Å2 / Biso mean: 35.6206 Å2 / Biso min: 10.32 Å2
Refinement stepCycle: final / Resolution: 1.911→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 0 428 5016
Biso mean---40.27 -
Num. residues----565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074687
X-RAY DIFFRACTIONf_angle_d1.026330
X-RAY DIFFRACTIONf_chiral_restr0.041676
X-RAY DIFFRACTIONf_plane_restr0.004819
X-RAY DIFFRACTIONf_dihedral_angle_d14.4421758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.911-1.94760.29471250.2651251991
1.9476-1.98740.29821290.2495260793
1.9874-2.03060.29741350.2312262594
2.0306-2.07790.29311400.2269265096
2.0779-2.12980.23791400.2028268197
2.1298-2.18740.25621450.1889270497
2.1874-2.25180.22561360.1828269597
2.2518-2.32450.22521470.1644271497
2.3245-2.40750.20291370.1665276498
2.4075-2.50390.21151560.1553271798
2.5039-2.61790.18941620.1586274999
2.6179-2.75590.21281250.1699279699
2.7559-2.92850.20341330.1661281499
2.9285-3.15460.24131510.1755280499
3.1546-3.4720.20851460.16092839100
3.472-3.97420.20561620.14012851100
3.9742-5.00630.15091580.12022901100
5.0063-49.250.17891560.14493061100
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)
11.70370.25280.3842.46750.33052.0287-0.03290.2845-0.0221-0.15480.0774-0.9197-0.00220.89220.03960.26430.02180.03640.4533-0.040.433363.569-13.3813-8.0144
21.865-0.6351-0.17141.78860.11421.8567-0.1251-0.10490.6886-0.1044-0.07080.0986-0.80040.12330.16690.3965-0.0502-0.05480.1493-0.01570.306747.33710.62470.5278
31.2683-0.15420.36481.06520.16261.3863-0.0709-0.21120.28880.0873-0.0514-0.0252-0.3186-0.13340.15180.23690.0314-0.03420.1811-0.06180.190943.34673.21099.559
41.69670.05670.55232.00380.20811.2409-0.122-0.64120.45510.1719-0.20090.2364-0.2429-0.52780.01280.29790.04890.01620.4624-0.15930.233534.74583.054916.9773
52.6519-0.71090.19861.88150.47662.107-0.018-0.42610.06890.0674-0.02550.1096-0.0269-0.31010.04630.18960.0079-0.02490.2049-0.03380.121138.5109-5.296810.8702
68.8023-3.40112.43462.2168-1.17743.41330.28230.1749-0.6187-0.1191-0.10130.37550.1713-0.0518-0.12140.184-0.0249-0.01970.1091-0.02080.158138.5519-13.80172.2868
73.62580.7753-0.25171.4219-0.36620.9848-0.0615-0.01480.2596-0.00950.05520.10150.0591-0.18180.14110.1753-0.0044-0.02880.1507-0.0120.158841.1926-2.18272.711
82.0125-0.08831.38562.5821.8766.24130.13770.0104-0.238-0.2335-0.16950.0730.1771-0.29030.04990.15320.003-0.00980.12440.00050.143846.5532-12.6664-5.0323
92.5089-0.15470.64431.3941-0.60771.6158-0.01040.07460.0574-0.1779-0.0555-0.2746-0.05620.24540.09340.1292-0.0061-0.00070.14720.02310.124754.8772-5.585-6.4875
103.79451.85240.41694.36480.17852.0473-0.09260.1077-0.48120.0021-0.0403-0.09190.47450.108-0.1620.2590.04420.00690.1317-0.01580.207152.5022-20.9023-2.3504
112.48180.42860.25072.3131-0.91351.03050.0599-0.1706-0.27740.09280.01830.20940.15-0.2506-0.16120.2878-0.0781-0.03250.32740.05950.255422.311-23.24988.4912
121.9082-0.5550.85521.8715-1.49983.1102-0.0331-0.0627-0.0836-0.07970.12680.16170.0367-0.3509-0.00740.17610.009-0.00590.1885-0.06870.234511.02-2.9259-13.5388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1212 through 1258 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1259 through 1309 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1310 through 1348 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1349 through 1374 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1375 through 1413 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1414 through 1429 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1430 through 1445 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1446 through 1463 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1464 through 1485 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 1486 through 1507 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 807 through 904 )B807 - 904
12X-RAY DIFFRACTION12chain 'B' and (resid 905 through 1114 )B905 - 1114

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