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- PDB-8a1f: Human PTPRK N-terminal domains MAM-Ig-FN1 -

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Basic information

Entry
Database: PDB / ID: 8a1f
TitleHuman PTPRK N-terminal domains MAM-Ig-FN1
ComponentsReceptor-type tyrosine-protein phosphatase kappa
KeywordsCELL ADHESION / Receptor phosphatase / homophilic complex
Function / homology
Function and homology information


gamma-catenin binding / transmembrane receptor protein tyrosine phosphatase activity / leading edge membrane / focal adhesion assembly / protein localization to cell surface / negative regulation of cell cycle / negative regulation of keratinocyte proliferation / protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase ...gamma-catenin binding / transmembrane receptor protein tyrosine phosphatase activity / leading edge membrane / focal adhesion assembly / protein localization to cell surface / negative regulation of cell cycle / negative regulation of keratinocyte proliferation / protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / cellular response to reactive oxygen species / adherens junction / EGFR downregulation / beta-catenin binding / neuron projection development / cellular response to UV / cell junction / cell-cell junction / cell migration / cell adhesion / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / protein kinase binding / cell surface / signal transduction / membrane / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase U Fn3 domain / MAM domain signature. / : / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase ...Receptor-type tyrosine-protein phosphatase U Fn3 domain / MAM domain signature. / : / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set 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 / Jelly Rolls - #200 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase kappa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHay, I.M. / Graham, S.C. / Sharpe, H.J. / Deane, J.E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust109407/Z/15/Z United Kingdom
Wellcome Trust219447/Z/19/Z United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Determinants of receptor tyrosine phosphatase homophilic adhesion: Structural comparison of PTPRK and PTPRM extracellular domains.
Authors: Hay, I.M. / Shamin, M. / Caroe, E.R. / Mohammed, A.S.A. / Svergun, D.I. / Jeffries, C.M. / Graham, S.C. / Sharpe, H.J. / Deane, J.E.
History
DepositionJun 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase kappa
B: Receptor-type tyrosine-protein phosphatase kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,61310
Polymers82,7942
Non-polymers2,8198
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.790, 93.862, 181.737
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 32 through 387 or resid 1005 through 1006 or resid 1009 through 2001))
d_2ens_1(chain "B" and (resid 32 through 220 or resid 226...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERTHRA2 - 352
d_12ens_1NAGNAGE
d_13ens_1NAGNAGF
d_14ens_1NAGNAGI
d_21ens_1SERGLYK1 - 189
d_22ens_1ASNTHRK191 - 352
d_23ens_1NAGNAGE
d_24ens_1NAGNAGF
d_25ens_1NAGNAGB

NCS oper: (Code: givenMatrix: (-0.0685288151742, -0.9899693746, -0.123549337693), (-0.991234028204, 0.0535426248905, 0.120781988106), (-0.112955313385, 0.130743354222, -0.984960543628)Vector: 69. ...NCS oper: (Code: given
Matrix: (-0.0685288151742, -0.9899693746, -0.123549337693), (-0.991234028204, 0.0535426248905, 0.120781988106), (-0.112955313385, 0.130743354222, -0.984960543628)
Vector: 69.738330351, 60.8156952245, 45.3886862288)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Receptor-type tyrosine-protein phosphatase kappa / Protein-tyrosine phosphatase kappa / R-PTP-kappa


Mass: 41397.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRK, PTPK / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) / References: UniProt: Q15262, protein-tyrosine-phosphatase

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Sugars , 5 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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

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Non-polymers , 2 types, 4 molecules

#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 4.52 Å3/Da / Density % sol: 72.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES, pH 7, 10% (w/v) polyethylene glycol (PEG) 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 3→79.05 Å / Num. obs: 30882 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 111.24 Å2 / CC1/2: 1 / Net I/σ(I): 18.7
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 1502 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
DIALSdata scaling
Cootmodel building
DIALSdata reduction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V5Y

2v5y


Resolution: 3→60.46 Å / SU ML: 0.4045 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2738 1626 5.28 %
Rwork0.2277 29183 -
obs0.23 30809 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.93 Å2
Refinement stepCycle: LAST / Resolution: 3→60.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5543 0 185 2 5730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325873
X-RAY DIFFRACTIONf_angle_d0.7358008
X-RAY DIFFRACTIONf_chiral_restr0.0472907
X-RAY DIFFRACTIONf_plane_restr0.00661039
X-RAY DIFFRACTIONf_dihedral_angle_d12.93082193
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.9815483003 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.090.33871260.30272366X-RAY DIFFRACTION99.36
3.09-3.190.38331130.37262416X-RAY DIFFRACTION100
3.19-3.30.48821290.3562416X-RAY DIFFRACTION99.96
3.3-3.430.38991640.2932352X-RAY DIFFRACTION99.92
3.43-3.590.3341400.24472412X-RAY DIFFRACTION100
3.59-3.780.28131280.24062432X-RAY DIFFRACTION100
3.78-4.010.26871480.25622393X-RAY DIFFRACTION100
4.01-4.320.26171520.19262390X-RAY DIFFRACTION100
4.33-4.760.20451250.17622469X-RAY DIFFRACTION100
4.76-5.450.18231340.17942445X-RAY DIFFRACTION100
5.45-6.860.27741220.22552497X-RAY DIFFRACTION100
6.86-60.460.2931450.23892595X-RAY DIFFRACTION99.6
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)
14.231315992622.0679104043-2.428901374554.191879524-2.534808665058.00277538919-0.2296107110090.01669073461390.032218277328-0.07558773072090.1954101519050.09768041219330.08923609576450.146713405333-0.009933343168230.5657787747030.0535277346734-0.03208978903490.488949289998-0.1469391085730.70325896297510.155228847113.195763142651.1070221496
29.425727300046.59108395226-2.704582669054.86151648006-2.165546880962.898490431040.584401942316-1.037454668920.3754875698060.766051467288-0.924669616886-0.138338032376-0.63911577450.7688281004450.2616876773521.36645430051-0.597432901962-0.2578663564881.33580974460.1915845167051.008171377147.711403719247.563426969625.672123049
33.139042449512.21937536481-2.777738396125.31270396861-4.061515934537.451330461630.288570568295-0.210189788522-0.003023904113110.230903378112-0.317005587805-0.0948500361490.2551081768860.377883428149-0.01753722923880.5802496512490.0327706734887-0.1682607706620.6386680212410.02713304308720.73919773138849.712584394957.6175041838-4.35731937525
48.178869788817.3057574748-2.8809707476.89401126513-2.407236873086.33005628229-0.7311383366830.6165067451950.413551289706-0.9650056606730.5693699961230.41216023540.149468891171-0.2500951144450.1677516074390.992380630597-0.245936250721-0.04958329676530.800565130367-0.02214777695920.86610181037316.386473890219.745095909520.5222210061
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 31 through 289 )AA31 - 2891 - 254
22chain 'A' and (resid 290 through 388 )AA290 - 388255 - 353
33chain 'B' and (resid 32 through 289 )BK32 - 2891 - 254
44chain 'B' and (resid 290 through 387 )BK290 - 387255 - 352

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