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- PDB-5fn7: Crystal structure of human CD45 extracellular region, domains d1-d2 -

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Entry
Database: PDB / ID: 5fn7
TitleCrystal structure of human CD45 extracellular region, domains d1-d2
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
KeywordsHYDROLASE / RECEPTOR PROTEIN TYROSINE PHOSPHATASE C / CD45 / PTPRC
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 / 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 / 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 ...Receptor-type tyrosine-protein phosphatase C / Protein tyrosine phosphatase, receptor type, N-terminal / Protein tyrosine phosphatase N terminal / Leukocyte receptor CD45 / 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 C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsChang, V.T. / Fernandes, R.A. / Ganzinger, K.A. / Lee, S.F. / Siebold, C. / McColl, J. / Jonsson, P. / Palayret, M. / Harlos, K. / Coles, C.H. ...Chang, V.T. / Fernandes, R.A. / Ganzinger, K.A. / Lee, S.F. / Siebold, C. / McColl, J. / Jonsson, P. / Palayret, M. / Harlos, K. / Coles, C.H. / Jones, E.Y. / Lui, Y. / Huang, E. / Gilbert, R.J.C. / Klenerman, D. / Aricescu, A.R. / Davis, S.J.
CitationJournal: Nat.Immunol. / Year: 2016
Title: Initiation of T Cell Signaling by Cd45 Segregation at 'Close Contacts'.
Authors: Chang, V.T. / Fernandes, R.A. / Ganzinger, K.A. / Lee, S.F. / Siebold, C. / Mccoll, J. / Jonsson, P. / Palayret, M. / Harlos, K. / Coles, C.H. / Jones, E.Y. / Lui, Y. / Huang, E. / Gilbert, ...Authors: Chang, V.T. / Fernandes, R.A. / Ganzinger, K.A. / Lee, S.F. / Siebold, C. / Mccoll, J. / Jonsson, P. / Palayret, M. / Harlos, K. / Coles, C.H. / Jones, E.Y. / Lui, Y. / Huang, E. / Gilbert, R.J. / Klenerman, D. / Aricescu, A.R. / Davis, S.J.
History
DepositionNov 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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 C
B: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,98813
Polymers42,5952
Non-polymers2,39211
Water1,892105
1
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5847
Polymers21,2981
Non-polymers1,2866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4046
Polymers21,2981
Non-polymers1,1065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.610, 149.610, 52.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C / LEUKOCYTE COMMON ANTIGEN / L-CA / T200 / CD45


Mass: 21297.725 Da / Num. of mol.: 2 / Fragment: DOMAINS D1-D2, RESIDUES 223-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-CELLS / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P08575, protein-tyrosine-phosphatase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsETGIEGR N-TERMINAL RESIDUES DERIVED FROM THE EXPRESSION VECTOR. GTKHHHHHH C-TERMINAL RESIDUES ...ETGIEGR N-TERMINAL RESIDUES DERIVED FROM THE EXPRESSION VECTOR. GTKHHHHHH C-TERMINAL RESIDUES DERIVED FROM THE EXPRESSION VECTOR.

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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: 4.26 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growpH: 8
Details: 0.1M TRIS, PH=8, 2.4M (NH4)2SO4, 6% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9497
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9497 Å / Relative weight: 1
ReflectionResolution: 2.3→43 Å / Num. obs: 30027 / % possible obs: 99.2 % / Observed criterion σ(I): 2.6 / Redundancy: 9.2 % / Biso Wilson estimate: 50.89 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→43 Å / Cor.coef. Fo:Fc: 0.9241 / Cor.coef. Fo:Fc free: 0.9112 / SU R Cruickshank DPI: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.187 / SU Rfree Blow DPI: 0.171 / SU Rfree Cruickshank DPI: 0.173
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=HG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2975. NUMBER WITH APPROX DEFAUL CCP4 ATOM TYPE=0. NUMBER ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=HG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2975. NUMBER WITH APPROX DEFAUL CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1524 5.08 %RANDOM
Rwork0.2015 ---
obs0.2033 30020 99.17 %-
Displacement parametersBiso mean: 58.89 Å2
Baniso -1Baniso -2Baniso -3
1--7.3634 Å20 Å20 Å2
2---7.3634 Å20 Å2
3---14.7268 Å2
Refine analyzeLuzzati coordinate error obs: 0.401 Å
Refinement stepCycle: LAST / Resolution: 2.3→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 128 105 2977
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012941HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.324007HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1078SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes410HARMONIC5
X-RAY DIFFRACTIONt_it2941HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion18.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion439SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3220SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2738 145 4.95 %
Rwork0.2463 2782 -
all0.2477 2927 -
obs--99.17 %
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)
11.17720.11061.25640.61641.31132.71620.0686-0.08060.11330.1108-0.1173-0.01260.24830.18310.0487-0.0299-0.19320.0217-0.07260.0558-0.09727.3305170.0242-22.4687
20.6668-0.33180.34741.84942.20344.2974-0.05510.0208-0.0807-0.19250.0120.08990.07170.39390.04310.0224-0.08630.0153-0.23860.0608-0.120814.9541147.0396-60.1529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - A|173 }
2X-RAY DIFFRACTION2{ B|2 - B|172 }

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