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- PDB-7u01: Structure of CD148 fibronectin type III domain 2 -

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Basic information

Entry
Database: PDB / ID: 7u01
TitleStructure of CD148 fibronectin type III domain 2
ComponentsReceptor-type tyrosine-protein phosphatase eta
KeywordsSIGNALING PROTEIN / receptor type protein tyrosine phosphatase
Function / homology
Function and homology information


contact inhibition / positive regulation of Fc receptor mediated stimulatory signaling pathway / gamma-catenin binding / delta-catenin binding / positive regulation of platelet activation / negative regulation of vascular permeability / platelet-derived growth factor receptor binding / mitogen-activated protein kinase binding / platelet formation / negative regulation of platelet-derived growth factor receptor signaling pathway ...contact inhibition / positive regulation of Fc receptor mediated stimulatory signaling pathway / gamma-catenin binding / delta-catenin binding / positive regulation of platelet activation / negative regulation of vascular permeability / platelet-derived growth factor receptor binding / mitogen-activated protein kinase binding / platelet formation / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of T cell receptor signaling pathway / positive chemotaxis / positive regulation of macrophage chemotaxis / Phosphorylation of CD3 and TCR zeta chains / negative regulation of epidermal growth factor receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / negative regulation of MAP kinase activity / phosphatase activity / peptidyl-tyrosine dephosphorylation / oligodendrocyte differentiation / immunological synapse / positive regulation of focal adhesion assembly / vasculogenesis / regulation of cell adhesion / specific granule membrane / protein-tyrosine-phosphatase / Negative regulation of FLT3 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell adhesion / negative regulation of insulin receptor signaling pathway / positive regulation of calcium-mediated signaling / protein tyrosine phosphatase activity / axon guidance / positive regulation of phagocytosis / negative regulation of cell migration / B cell differentiation / Negative regulation of MET activity / negative regulation of cell growth / beta-catenin binding / ruffle membrane / cytokine-mediated signaling pathway / blood coagulation / positive regulation of tumor necrosis factor production / cell-cell junction / cell junction / glucose homeostasis / T cell receptor signaling pathway / heart development / angiogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / nuclear body / cadherin binding / negative regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / nucleolus / cell surface / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / 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. ...PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29707910798 Å
AuthorsZhou, D. / Zhu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137143 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL131836 United States
CitationJournal: To Be Published
Title: Structure of CD148 fibronectin type III domain 1 and 2
Authors: Zhou, D. / Zhu, J.
History
DepositionFeb 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Receptor-type tyrosine-protein phosphatase eta
B: Receptor-type tyrosine-protein phosphatase eta
C: Receptor-type tyrosine-protein phosphatase eta
D: Receptor-type tyrosine-protein phosphatase eta


Theoretical massNumber of molelcules
Total (without water)67,8334
Polymers67,8334
Non-polymers00
Water1,63991
1
A: Receptor-type tyrosine-protein phosphatase eta


Theoretical massNumber of molelcules
Total (without water)16,9581
Polymers16,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Receptor-type tyrosine-protein phosphatase eta


Theoretical massNumber of molelcules
Total (without water)16,9581
Polymers16,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Receptor-type tyrosine-protein phosphatase eta


Theoretical massNumber of molelcules
Total (without water)16,9581
Polymers16,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Receptor-type tyrosine-protein phosphatase eta


Theoretical massNumber of molelcules
Total (without water)16,9581
Polymers16,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.068, 155.068, 47.837
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11D-417-

HOH

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Components

#1: Protein
Receptor-type tyrosine-protein phosphatase eta / Protein-tyrosine phosphatase eta / R-PTP-eta / Density-enhanced phosphatase 1 / DEP-1 / HPTP eta / ...Protein-tyrosine phosphatase eta / R-PTP-eta / Density-enhanced phosphatase 1 / DEP-1 / HPTP eta / Protein-tyrosine phosphatase receptor type J / R-PTP-J / CD148


Mass: 16958.318 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRJ, DEP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12913, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M sodium acetate pH4.5, 3M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979276 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979276 Å / Relative weight: 1
ReflectionResolution: 2.297→50 Å / Num. obs: 26929 / % possible obs: 100 % / Redundancy: 26.6 % / Biso Wilson estimate: 54.4779195349 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.4
Reflection shellResolution: 2.2971→2.3545 Å / Rmerge(I) obs: 1.1 / Num. unique obs: 1712

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.29707910798→45.7113330479 Å / SU ML: 0.329266292209 / Cross valid method: FREE R-VALUE / σ(F): 1.35298695758 / Phase error: 31.7182115406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.260416175608 1997 7.50526157547 %
Rwork0.213740512015 24611 -
obs0.21719288275 26608 99.7750112494 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.786072096 Å2
Refinement stepCycle: LAST / Resolution: 2.29707910798→45.7113330479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 0 92 3268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002405110036483216
X-RAY DIFFRACTIONf_angle_d0.5909772206864365
X-RAY DIFFRACTIONf_chiral_restr0.0408243326667509
X-RAY DIFFRACTIONf_plane_restr0.00319951637898576
X-RAY DIFFRACTIONf_dihedral_angle_d2.768918487621961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2971-2.35450.3813422328441390.3572496934961712X-RAY DIFFRACTION99.9460043197
2.3545-2.41820.3877680835361410.3083952677841730X-RAY DIFFRACTION99.8932194341
2.4182-2.48930.3537311364771400.2969143973321733X-RAY DIFFRACTION99.8933333333
2.4893-2.56970.3335538534671410.2819004471791729X-RAY DIFFRACTION99.8931623932
2.5697-2.66150.2958119117751410.2724511367611742X-RAY DIFFRACTION99.8409331919
2.6615-2.76810.3521415932231390.2419614393951709X-RAY DIFFRACTION99.8379254457
2.7681-2.8940.3359428801671410.2360713085931748X-RAY DIFFRACTION99.9470899471
2.894-3.04660.2863703497241430.2275240616621751X-RAY DIFFRACTION99.9472295515
3.0466-3.23740.2897782816951420.2250936521371753X-RAY DIFFRACTION99.947257384
3.2374-3.48730.2703697543421400.211735532211741X-RAY DIFFRACTION99.6820349762
3.4873-3.83810.2316843420751430.2050035389511764X-RAY DIFFRACTION99.6342737722
3.8381-4.3930.2338389782511460.1777798005181797X-RAY DIFFRACTION99.9485596708
4.393-5.53320.2127825132311460.1709116378871798X-RAY DIFFRACTION100
5.5332-45.71130.2348091572861550.2237605178481904X-RAY DIFFRACTION98.6583612841
Refinement TLS params.Method: refined / Origin x: 116.185225815 Å / Origin y: 76.2849144805 Å / Origin z: 19.365837285 Å
111213212223313233
T0.362082306195 Å20.00886849199474 Å2-0.00353137135254 Å2-0.379996828523 Å2-0.00925790505182 Å2--0.471913286099 Å2
L0.618048869213 °2-0.123792942192 °2-0.104443769088 °2-0.896395608605 °2-0.0308928309483 °2--0.783823667811 °2
S-0.0118086353143 Å °0.100834544786 Å °0.0641074441785 Å °0.0738865085607 Å °-0.088168575684 Å °0.110729889667 Å °-0.0672926782885 Å °0.0208667303896 Å °0.0920390127626 Å °
Refinement TLS groupSelection details: all

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