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- PDB-7u08: Structure of CD148 fibronectin type III domain 1 and 2 -

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Basic information

Entry
Database: PDB / ID: 7u08
TitleStructure of CD148 fibronectin type III domain 1 and 2
ComponentsReceptor-type tyrosine-protein phosphatase eta
KeywordsSIGNALING PROTEIN / receptor type protein tyrosine phosphatase
Function / homology
Function and homology information


positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / platelet-derived growth factor receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of vascular permeability / mitogen-activated protein kinase binding / negative regulation of T cell receptor signaling pathway / positive chemotaxis ...positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / platelet-derived growth factor receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of vascular permeability / mitogen-activated protein kinase binding / negative regulation of T cell receptor signaling pathway / positive chemotaxis / negative regulation of epidermal growth factor receptor signaling pathway / Phosphorylation of CD3 and TCR zeta chains / phosphatase activity / positive regulation of focal adhesion assembly / platelet-derived growth factor receptor signaling pathway / : / immunological synapse / peptidyl-tyrosine dephosphorylation / positive regulation of cell adhesion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / specific granule membrane / positive regulation of phagocytosis / regulation of cell adhesion / Negative regulation of FLT3 / B cell differentiation / protein-tyrosine-phosphatase / negative regulation of cell migration / negative regulation of MAP kinase activity / protein tyrosine phosphatase activity / Negative regulation of MET activity / negative regulation of cell growth / beta-catenin binding / ruffle membrane / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / positive regulation of tumor necrosis factor production / T cell receptor signaling pathway / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cadherin binding / negative regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / cell surface / extracellular exosome / 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. / Protein-tyrosine phosphatase, 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 / Tyrosine specific protein phosphatases domain profile. / 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: 3.30691735712 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9252
Polymers35,7301
Non-polymers1951
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.325, 142.325, 57.722
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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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


Mass: 35729.773 Da / Num. of mol.: 1
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: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.25M MgCl2, 0.1M HEPES pH7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 5502 / % possible obs: 100 % / Redundancy: 38.8 % / Biso Wilson estimate: 135.736775868 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 34.3
Reflection shellResolution: 3.3→3.36 Å / Num. unique obs: 258 / CC1/2: 0.235

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
HKL-3000data reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.30691735712→19.7369263569 Å / SU ML: 0.48564175729 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.8756769017
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.300255629433 533 10.0832387439 %
Rwork0.267545001521 4753 -
obs0.270966472295 5286 96.6538672518 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 155.859958037 Å2
Refinement stepCycle: LAST / Resolution: 3.30691735712→19.7369263569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 1 0 1488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004404286080151518
X-RAY DIFFRACTIONf_angle_d0.830443047192070
X-RAY DIFFRACTIONf_chiral_restr0.0539660978623242
X-RAY DIFFRACTIONf_plane_restr0.00635272818748264
X-RAY DIFFRACTIONf_dihedral_angle_d5.81464946838913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.307-3.63780.4121259315591250.3963239032581080X-RAY DIFFRACTION91.1497730711
3.6378-4.15990.3566163795111290.3139025743871158X-RAY DIFFRACTION95.9731543624
4.1599-5.22490.2550839064031340.2386310185441213X-RAY DIFFRACTION99.1899852725
5.2249-19.73690.2949542096041450.2527648040231302X-RAY DIFFRACTION99.9309392265
Refinement TLS params.Method: refined / Origin x: 30.1465290208 Å / Origin y: 40.7807218104 Å / Origin z: 31.6548398961 Å
111213212223313233
T1.04589640142 Å2-0.0165951054802 Å2-0.107698053871 Å2-1.16473613648 Å20.0270084980935 Å2--1.11227113997 Å2
L7.27144528798 °2-1.85871080546 °20.194311151354 °2-6.44698601741 °21.1851798449 °2--2.60354930694 °2
S-0.258246180294 Å °-0.489759165975 Å °0.134331474718 Å °0.940662319048 Å °-0.205767813443 Å °0.39505131928 Å °0.181331756259 Å °-0.0594146418109 Å °0.552523899631 Å °
Refinement TLS groupSelection details: all

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