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- PDB-1ygu: Crystal structure of the tandem phosphatase domains of RPTP CD45 ... -

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Basic information

Entry
Database: PDB / ID: 1ygu
TitleCrystal structure of the tandem phosphatase domains of RPTP CD45 with a pTyr peptide
Components
  • Leukocyte common antigenPTPRC
  • Polyoma Middle T antigen
KeywordsHYDROLASE / CD45 / protein tyrosine phosphatase / phosphotyrosine / polyoma middle T antigen / RPTP
Function / homology
Function and homology information


plasma membrane raft distribution / positive regulation of antigen receptor-mediated signaling pathway / membrane microdomain / regulation of protein tyrosine kinase activity / positive regulation of protein tyrosine phosphatase activity / positive regulation of hematopoietic stem cell migration / negative regulation of cytokine-mediated signaling pathway / alpha-beta T cell proliferation / negative regulation of protein tyrosine kinase activity / positive regulation of Fc receptor mediated stimulatory signaling pathway ...plasma membrane raft distribution / positive regulation of antigen receptor-mediated signaling pathway / membrane microdomain / regulation of protein tyrosine kinase activity / positive regulation of protein tyrosine phosphatase activity / positive regulation of hematopoietic stem cell migration / negative regulation of cytokine-mediated signaling pathway / alpha-beta T cell proliferation / negative regulation of protein tyrosine kinase activity / positive regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of cell adhesion involved in substrate-bound cell migration / regulation of interleukin-8 production / negative regulation of microglial cell activation / Other semaphorin interactions / negative regulation of T cell mediated cytotoxicity / positive regulation of humoral immune response mediated by circulating immunoglobulin / DN2 thymocyte differentiation / cell cycle phase transition / negative regulation of protein autophosphorylation / gamma-delta T cell differentiation / natural killer cell differentiation / positive regulation of gamma-delta T cell differentiation / transmembrane receptor protein tyrosine phosphatase activity / : / bleb / positive regulation of alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / stem cell development / heparan sulfate proteoglycan binding / positive thymic T cell selection / regulation of phagocytosis / positive regulation of extrinsic apoptotic signaling pathway / heterotypic cell-cell adhesion / bone marrow development / regulation of receptor signaling pathway via JAK-STAT / negative regulation of interleukin-2 production / ankyrin binding / leukocyte cell-cell adhesion / spectrin binding / response to aldosterone / positive regulation of stem cell proliferation / Phosphorylation of CD3 and TCR zeta chains / B cell proliferation / : / positive regulation of immunoglobulin production / T cell differentiation / host cell membrane / positive regulation of protein kinase activity / hematopoietic progenitor cell differentiation / positive regulation of phagocytosis / dephosphorylation / positive regulation of B cell proliferation / extrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / T cell activation / protein dephosphorylation / B cell differentiation / protein-tyrosine-phosphatase / secretory granule membrane / protein tyrosine phosphatase activity / response to gamma radiation / B cell receptor signaling pathway / negative regulation of protein kinase activity / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of T cell mediated cytotoxicity / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / heparin binding / T cell receptor signaling pathway / regulation of gene expression / defense response to virus / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / regulation of cell cycle / membrane raft / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / protein kinase binding / cell surface / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase C / Protein tyrosine phosphatase, receptor type, N-terminal / Protein tyrosine phosphatase N terminal / Leukocyte receptor CD45 / Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / DnaJ molecular chaperone homology domain / Chaperone J-domain superfamily / DnaJ domain ...Receptor-type tyrosine-protein phosphatase C / Protein tyrosine phosphatase, receptor type, N-terminal / Protein tyrosine phosphatase N terminal / Leukocyte receptor CD45 / Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / DnaJ molecular chaperone homology domain / Chaperone J-domain superfamily / DnaJ domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Middle T antigen / Receptor-type tyrosine-protein phosphatase C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNam, H. / Poy, F. / Saito, H. / Frederick, C.A.
CitationJournal: J.Exp.Med. / Year: 2005
Title: Structural basis for the function and regulation of the receptor protein tyrosine phosphatase CD45.
Authors: Nam, H.J. / Poy, F. / Saito, H. / Frederick, C.A.
History
DepositionJan 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukocyte common antigen
B: Leukocyte common antigen
C: Polyoma Middle T antigen
D: Polyoma Middle T antigen


Theoretical massNumber of molelcules
Total (without water)144,0944
Polymers144,0944
Non-polymers00
Water0
1
A: Leukocyte common antigen
C: Polyoma Middle T antigen


Theoretical massNumber of molelcules
Total (without water)72,0472
Polymers72,0472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-6 kcal/mol
Surface area25250 Å2
MethodPISA
2
B: Leukocyte common antigen
D: Polyoma Middle T antigen


Theoretical massNumber of molelcules
Total (without water)72,0472
Polymers72,0472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-6 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.900, 57.920, 159.290
Angle α, β, γ (deg.)90.00, 98.66, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTwo biological units are present in an asymmetric unit.

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Components

#1: Protein Leukocyte common antigen / PTPRC / L-CA / CD45 antigen / T200


Mass: 71500.625 Da / Num. of mol.: 2 / Fragment: D1 and D2 PTP domains / Mutation: C828S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRC, CD45 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08575, protein-tyrosine-phosphatase
#2: Protein/peptide Polyoma Middle T antigen


Mass: 546.464 Da / Num. of mol.: 2 / Fragment: Middle T antigen (residues 248-251, SWS:P03077) / Source method: obtained synthetically / Details: Polyoma Middle T antigen pTyr peptide / References: UniProt: P03077

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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: 2.9 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, sodium acetate, glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 3, 2003
RadiationMonochromator: channel cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 34492 / Num. obs: 32025 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 57.5 Å2 / Rsym value: 0.079 / Net I/σ(I): 17.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2268 / % possible all: 67

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D2 domain of RPTP LAR

Resolution: 2.9→29.16 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1758427.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1588 5 %RANDOM
Rwork0.262 ---
all0.265 34492 --
obs0.262 32025 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.2085 Å2 / ksol: 0.28125 e/Å3
Displacement parametersBiso mean: 78 Å2
Baniso -1Baniso -2Baniso -3
1--12.51 Å20 Å2-25.93 Å2
2--41.82 Å20 Å2
3----29.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.51 Å
Luzzati d res low-30 Å
Luzzati sigma a0.91 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9531 0 0 0 9531
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.466 195 4.9 %
Rwork0.434 3804 -
obs--70.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAMPTY.TOP
X-RAY DIFFRACTION4PTY_MOD.PARION.TOP

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