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- PDB-5fn8: Crystal structure of rat CD45 extracellular region, domains d3-d4 -

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Basic information

Entry
Database: PDB / ID: 5fn8
TitleCrystal structure of rat CD45 extracellular region, domains d3-d4
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
KeywordsHYDROLASE / RECEPTOR PROTEIN TYROSINE PHOSPHATASE C / CD45 / PTPRC
Function / homology
Function and homology information


regulation of humoral immune response mediated by circulating immunoglobulin / Other semaphorin interactions / positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / Phosphorylation of CD3 and TCR zeta chains / 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 ...regulation of humoral immune response mediated by circulating immunoglobulin / Other semaphorin interactions / positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / Phosphorylation of CD3 and TCR zeta chains / 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 / negative regulation of protein tyrosine kinase activity / regulation of extrinsic apoptotic signaling pathway / : / negative regulation of cell adhesion involved in substrate-bound cell migration / regulation of interleukin-8 production / negative regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell mediated immunity / negative regulation of T cell mediated cytotoxicity / positive regulation of humoral immune response mediated by circulating immunoglobulin / cell cycle phase transition / negative regulation of protein autophosphorylation / 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 / protein kinase regulator activity / 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 / positive regulation of T cell differentiation / Neutrophil degranulation / negative regulation of interleukin-2 production / ankyrin binding / leukocyte cell-cell adhesion / spectrin binding / positive regulation of stem cell proliferation / B cell proliferation / plasma membrane => GO:0005886 / : / T cell differentiation / hematopoietic progenitor cell differentiation / T cell proliferation / dephosphorylation / positive regulation of B cell proliferation / release of sequestered calcium ion into cytosol / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / protein dephosphorylation / B cell differentiation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell periphery / 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 / 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 / membrane => GO:0016020 / positive regulation of ERK1 and ERK2 cascade / regulation of cell cycle / membrane raft / external side of plasma membrane / signaling receptor binding / focal adhesion / protein kinase binding / cell surface / 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
CITRATE ANION / Receptor-type tyrosine-protein phosphatase C
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 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 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references / Other / Refinement description
Revision 1.3May 4, 2016Group: Database references
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

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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)44,3909
Polymers42,8742
Non-polymers1,5167
Water1,00956
1
B: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)44,2018
Polymers42,8742
Non-polymers1,3276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area10250 Å2
ΔGint-42.2 kcal/mol
Surface area21470 Å2
MethodPISA
2
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)44,57910
Polymers42,8742
Non-polymers1,7058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area10780 Å2
ΔGint-39.9 kcal/mol
Surface area21450 Å2
MethodPISA
3
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2905
Polymers21,4371
Non-polymers8534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1014
Polymers21,4371
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.410, 131.160, 141.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 21436.959 Da / Num. of mol.: 2
Fragment: EXTRACELLULAR REGION DOMAINS D3-D4, RESIDUES 357-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: THYMUS / Plasmid: PEE14 / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P04157, 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.: 6
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-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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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: 4.89 Å3/Da / Density % sol: 75 % / Description: NONE
Crystal growpH: 4.2
Details: 10% V/V 2-PROPANOL, 0.2M LISO4, 0.1M SODIUM PHOSPHATE-CITRATE, PH=4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0714
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0714 Å / Relative weight: 1
ReflectionResolution: 2.45→96 Å / Num. obs: 29113 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 4.8 % / Biso Wilson estimate: 79.47 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.9
Reflection shellResolution: 2.45→2.52 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
xia2data reduction
xia2data scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.45→30.65 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.9263 / SU R Cruickshank DPI: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.184
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY THE CORRECT OLIGOMERIC STATE OF THIS CONSTRUCT IS MONOMERIC, HOWEVER IT CRYSTALLIZED AS A DIMER DUE TO D3 DOMAIN SWAPPING
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1459 5.01 %RANDOM
Rwork0.2144 ---
obs0.2155 29106 99.67 %-
Displacement parametersBiso mean: 80.8 Å2
Baniso -1Baniso -2Baniso -3
1--10.034 Å20 Å20 Å2
2--2.5354 Å20 Å2
3---7.4986 Å2
Refine analyzeLuzzati coordinate error obs: 0.505 Å
Refinement stepCycle: LAST / Resolution: 2.45→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 97 56 2975
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012996HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.224077HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1029SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes433HARMONIC5
X-RAY DIFFRACTIONt_it2996HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion19.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion408SEMIHARMONIC5
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_contact3151SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.54 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.236 134 4.78 %
Rwork0.2715 2670 -
all0.2698 2804 -
obs--99.67 %
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)
11.893-0.0882-1.1280.6922-0.27032.6654-0.1040.03080.1224-0.0539-0.25090.0883-0.08130.07610.3549-0.07570.15680.0043-0.1675-0.0178-0.134336.87125.758943.1587
22.4397-1.2827-0.49622.66990.02370.7153-0.0730.16630.0033-0.00940.33650.0869-0.12080.0913-0.2636-0.0344-0.01410.2347-0.2043-0.0216-0.18625.469923.989864.2706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|3 - A|187 }
2X-RAY DIFFRACTION2{ B|3 - B|187 }

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