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- PDB-5fmv: Crystal structure of human CD45 extracellular region, domains d1-d4 -

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Basic information

Entry
Database: PDB / ID: 5fmv
TitleCrystal structure of human CD45 extracellular region, domains d1-d4
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
KeywordsHYDROLASE / RECEPTOR PROTEIN TYROSINE PHOSPHATASE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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 9, 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 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
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)86,21518
Polymers83,3012
Non-polymers2,91416
Water0
1
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0459
Polymers41,6511
Non-polymers1,3948
Water0
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)43,1709
Polymers41,6511
Non-polymers1,5198
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.550, 59.410, 100.420
Angle α, β, γ (deg.)90.00, 111.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C / LEUKOCYTE COMMON ANTIGEN / L-CA / T200 / CD45 EXTRACELLULAR REGION D1-D4


Mass: 41650.668 Da / Num. of mol.: 2 / Fragment: DOMAINS D1-D4, RESIDUES 223-571
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-CELLS / Plasmid: PEE14 / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / 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.: 11
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
Sequence detailsETG N-TERMINAL RESIDUES DERIVED FROM THE EXPRESSION VECTOR. GTKHHHHHH C-TERMINAL RESIDUES DERIVED ...ETG 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: 3.28 Å3/Da / Density % sol: 62.48 % / Description: NONE
Crystal growpH: 8 / Details: 14% W/V PEG8K, 0.2M (NH4)2SO4, PH=8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 22973 / % possible obs: 98.6 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Biso Wilson estimate: 75.35 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.9
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN CD45 EXTRACELLULAR REGION DOMAINS D1- D3

Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.8786 / Cor.coef. Fo:Fc free: 0.8173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.358
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1161 5.14 %RANDOM
Rwork0.2259 ---
obs0.2271 22584 96.79 %-
Displacement parametersBiso mean: 107.38 Å2
Baniso -1Baniso -2Baniso -3
1-12.336 Å20 Å28.2287 Å2
2--27.8747 Å20 Å2
3----40.2107 Å2
Refine analyzeLuzzati coordinate error obs: 0.601 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5632 0 179 0 5811
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085970HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.158128HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2779SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes174HARMONIC2
X-RAY DIFFRACTIONt_gen_planes849HARMONIC5
X-RAY DIFFRACTIONt_it5970HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion3.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion827SEMIHARMONIC5
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_contact5964SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.04 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2945 128 4.72 %
Rwork0.2601 2585 -
all0.2617 2713 -
obs--96.79 %
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)
10.1936-0.84921.75123.59391.0293.6147-0.0416-0.05950.08170.0107-0.0023-0.0893-0.0562-0.09040.04390.07370.3532-0.22920.0012-0.1368-0.0479-34.580461.019-2.8435
22.3716-0.69571.37250-0.42532.8581-0.0358-0.11150.03160.0938-0.00840.13690.0675-0.02870.0442-0.05810.4308-0.3810.16530.0228-0.1017-19.5837.91679.0631
32.7063-2.30833.23611.2546-0.28353.63590.11320.5234-0.0622-0.6726-0.13470.3877-0.1732-0.66230.0214-0.06350.1291-0.36240.13330.05470.01131.2606-0.087418.2731
43.8481-1.08170.15654.93250.14631.91050.0337-0.0405-0.1598-0.32660.07520.11790.2085-0.1203-0.1089-0.0541-0.0930.065-0.2037-0.0137-0.048427.225-23.456444.4434
56.1751-3.769-2.99445.0685-0.5136-0.87160.0026-0.0804-0.1362-0.1147-0.0507-0.40930.03170.35370.04810.0650.40660.08460.0777-0.20770.014156.6612-46.440121.0579
64.8032-3.3480.368412.0005-0.45252.7221-0.02230.25710.0826-0.10210.0169-0.1220.02040.14730.0054-0.12810.08810.1234-0.09870.0161-0.276339.2837-23.452227.0401
73.13-3.2177-0.55669.71722.29151.84960.26050.19470.1279-0.2602-0.0288-0.02780.04210.0423-0.2317-0.08090.09040.0104-0.08930.188-0.057316.282213.243826.587
88.7467-2.3735-1.02825.7534-0.67582.4864-0.10250.01310.06790.1192-0.00520.25070.07970.03760.1077-0.1809-0.06890.0651-0.3501-0.0230.2396-16.08836.605444.7014

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