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- PDB-1ygr: Crystal structure of the tandem phosphatase domain of RPTP CD45 -

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Basic information

Entry
Database: PDB / ID: 1ygr
TitleCrystal structure of the tandem phosphatase domain of RPTP CD45
Components
  • CD45 Protein Tyrosine Phosphatase
  • T-cell Receptor CD3 zeta ITAM-1
KeywordsHYDROLASE / Protein tyrosine Phosphatase / RPTP / CD45 / LCA / lymphocyte activation / CD3 zeta / ITAM
Function / homology
Function and homology information


plasma membrane raft distribution / positive regulation of antigen receptor-mediated signaling pathway / DN2 thymocyte differentiation / negative regulation of cell adhesion involved in substrate-bound cell migration / positive regulation of hematopoietic stem cell migration / regulation of T cell receptor signaling pathway / negative regulation of interleukin-4-mediated signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / membrane microdomain / negative regulation of T cell mediated cytotoxicity ...plasma membrane raft distribution / positive regulation of antigen receptor-mediated signaling pathway / DN2 thymocyte differentiation / negative regulation of cell adhesion involved in substrate-bound cell migration / positive regulation of hematopoietic stem cell migration / regulation of T cell receptor signaling pathway / negative regulation of interleukin-4-mediated signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / membrane microdomain / negative regulation of T cell mediated cytotoxicity / regulation of interleukin-8 production / negative regulation of microglial cell activation / stem cell development / natural killer cell differentiation / negative regulation of cytokine-mediated signaling pathway / Other semaphorin interactions / cell cycle phase transition / Fc-gamma receptor III complex / transmembrane receptor protein tyrosine phosphatase activity / Fc-gamma receptor signaling pathway / gamma-delta T cell activation / negative regulation of receptor signaling pathway via JAK-STAT / bleb / regulation of phagocytosis / response to aldosterone / positive regulation of stem cell proliferation / Nef and signal transduction / heparan sulfate proteoglycan binding / bone marrow development / alpha-beta T cell receptor complex / dephosphorylation / protein tyrosine kinase inhibitor activity / negative regulation of interleukin-2 production / protein dephosphorylation / ankyrin binding / T cell receptor complex / spectrin binding / positive regulation of immunoglobulin production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / B cell proliferation / positive regulation of protein kinase activity / protein complex oligomerization / alpha-beta T cell activation / hematopoietic progenitor cell differentiation / Generation of second messenger molecules / FCGR activation / T cell differentiation / Co-inhibition by PD-1 / Role of phospholipids in phagocytosis / release of sequestered calcium ion into cytosol / negative regulation of protein kinase activity / positive regulation of B cell proliferation / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / protein-tyrosine-phosphatase / B cell differentiation / positive regulation of T cell proliferation / response to gamma radiation / protein tyrosine phosphatase activity / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / protein tyrosine kinase binding / secretory granule membrane / B cell receptor signaling pathway / T cell activation / FCGR3A-mediated phagocytosis / negative regulation of ERK1 and ERK2 cascade / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cytoplasmic side of plasma membrane / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / T cell receptor signaling pathway / Downstream TCR signaling / heparin binding / regulation of gene expression / protein-containing complex assembly / defense response to virus / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / protein-macromolecule adaptor activity / regulation of cell cycle / cell surface receptor signaling pathway / membrane raft / protein heterodimerization activity / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / synapse / protein kinase binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / 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 / T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / : / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM ...Receptor-type tyrosine-protein phosphatase C / Protein tyrosine phosphatase, receptor type, N-terminal / Protein tyrosine phosphatase N terminal / Leukocyte receptor CD45 / T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / : / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / 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 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase C / T-cell surface glycoprotein CD3 zeta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNam, H.J. / 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 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Oct 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 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD45 Protein Tyrosine Phosphatase
B: CD45 Protein Tyrosine Phosphatase
C: T-cell Receptor CD3 zeta ITAM-1
D: T-cell Receptor CD3 zeta ITAM-1


Theoretical massNumber of molelcules
Total (without water)144,7834
Polymers144,7834
Non-polymers00
Water00
1
A: CD45 Protein Tyrosine Phosphatase
C: T-cell Receptor CD3 zeta ITAM-1


Theoretical massNumber of molelcules
Total (without water)72,3912
Polymers72,3912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-6 kcal/mol
Surface area26250 Å2
MethodPISA
2
B: CD45 Protein Tyrosine Phosphatase
D: T-cell Receptor CD3 zeta ITAM-1


Theoretical massNumber of molelcules
Total (without water)72,3912
Polymers72,3912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-6 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.010, 59.700, 160.530
Angle α, β, γ (deg.)90.00, 99.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CD45 Protein Tyrosine Phosphatase


Mass: 71500.625 Da / Num. of mol.: 2 / Fragment: Cytoplasmic domain / Mutation: C828S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08575
#2: Protein/peptide T-cell Receptor CD3 zeta ITAM-1


Mass: 890.808 Da / Num. of mol.: 2 / Fragment: ITAM-1 (residues 80-85; SWS:P20963) / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P20963
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Sodium acetate, PEG 4000, Glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0332 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→29.85 Å / Num. obs: 36165 / Biso Wilson estimate: 59.5 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.85 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2020965.81 / 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
Rfree0.312 1473 5 %RANDOM
Rwork0.255 ---
all0.261 36165 --
obs0.255 29453 81.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.7118 Å2 / ksol: 0.26757 e/Å3
Displacement parametersBiso mean: 83.2 Å2
Baniso -1Baniso -2Baniso -3
1--16.03 Å20 Å2-16.12 Å2
2--42.63 Å20 Å2
3----26.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.54 Å
Luzzati d res low-30 Å
Luzzati sigma a0.83 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9538 0 0 0 9538
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_d0.93
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.487 119 5.1 %
Rwork0.468 2234 -
obs--39.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PTY_MOD.PARPTY.TOP

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