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- PDB-8a16: Human PTPRM domains FN3-4, in spacegroup P212121 -

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Basic information

Entry
Database: PDB / ID: 8a16
TitleHuman PTPRM domains FN3-4, in spacegroup P212121
ComponentsReceptor-type tyrosine-protein phosphatase mu
KeywordsCELL ADHESION / Receptor phosphatase / homophilic dimer
Function / homology
Function and homology information


retina layer formation / transmembrane receptor protein tyrosine phosphatase activity / negative regulation of endothelial cell migration / retinal ganglion cell axon guidance / negative regulation of endothelial cell proliferation / homophilic cell adhesion via plasma membrane adhesion molecules / phosphatase activity / protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase ...retina layer formation / transmembrane receptor protein tyrosine phosphatase activity / negative regulation of endothelial cell migration / retinal ganglion cell axon guidance / negative regulation of endothelial cell proliferation / homophilic cell adhesion via plasma membrane adhesion molecules / phosphatase activity / 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 / negative regulation of angiogenesis / adherens junction / neuron projection development / cell-cell junction / lamellipodium / cadherin binding / response to xenobiotic stimulus / perinuclear region of cytoplasm / signal transduction / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Receptor-type tyrosine-protein phosphatase mu, PTPase domain, repeat 1 / 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. / Immunoglobulin / Immunoglobulin domain ...Receptor-type tyrosine-protein phosphatase mu, PTPase domain, repeat 1 / 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. / Immunoglobulin / Immunoglobulin domain / 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 subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsCaroe, E. / 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
DepositionMay 31, 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 1.2Oct 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,7685
Polymers57,8952
Non-polymers1,8743
Water00
1
A: Receptor-type tyrosine-protein phosphatase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6802
Polymers28,9471
Non-polymers7331
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0883
Polymers28,9471
Non-polymers1,1412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.682, 89.638, 128.289
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 481 through 723 or resid 725))
d_2ens_1(chain "B" and (resid 481 through 590 or resid 596...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUGLYA1 - 225
d_12ens_1NAGNAGB
d_21ens_1LEUALAB1 - 110
d_22ens_1PROGLUB116 - 148
d_23ens_1CYSGLYB162 - 243
d_24ens_1NAGNAGD

NCS oper: (Code: givenMatrix: (-0.975859186447, -0.212193319841, -0.0516995477927), (0.216163125295, -0.90461193933, -0.367356424312), (0.0311825510485, -0.369663677193, 0.928642242349)Vector: 27. ...NCS oper: (Code: given
Matrix: (-0.975859186447, -0.212193319841, -0.0516995477927), (0.216163125295, -0.90461193933, -0.367356424312), (0.0311825510485, -0.369663677193, 0.928642242349)
Vector: 27.6364460029, 49.3079156549, -24.7436379287)

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Components

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


Mass: 28947.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRM, PTPRL1 / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) / References: UniProt: P28827, protein-tyrosine-phosphatase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM ammonium nitrate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.89→128.29 Å / Num. obs: 13719 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 66.47 Å2 / CC1/2: 0.991 / Net I/σ(I): 7
Reflection shellResolution: 2.89→2.94 Å / Num. unique obs: 672 / CC1/2: 0.432

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Processing

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

2v5y


Resolution: 2.89→73.48 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.9403
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2881 674 4.94 %
Rwork0.2342 12962 -
obs0.2367 13636 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.76 Å2
Refinement stepCycle: LAST / Resolution: 2.89→73.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 125 0 3809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323913
X-RAY DIFFRACTIONf_angle_d0.77895338
X-RAY DIFFRACTIONf_chiral_restr0.0488619
X-RAY DIFFRACTIONf_plane_restr0.0059675
X-RAY DIFFRACTIONf_dihedral_angle_d12.80991439
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.22630686375 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.110.32071190.31282545X-RAY DIFFRACTION98.74
3.11-3.430.34371320.28782540X-RAY DIFFRACTION99.52
3.43-3.920.33841450.23472554X-RAY DIFFRACTION99.7
3.92-4.940.26631370.20182592X-RAY DIFFRACTION99.85
4.94-73.480.25311410.22152731X-RAY DIFFRACTION99.9
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)
10.8327595320130.605486448099-1.092825843591.5518955712-1.628763811013.749891590320.0408466622359-0.160322016563-0.003754448957270.120428619907-0.159771794693-0.116945720752-0.02561550104460.2889759285750.189095904560.375285246648-0.00555088347246-0.04263123018990.438177545605-0.01338508280670.4606881804466.3717378994331.463721720725.997756124
20.7067465358860.0454345084246-0.2846590962430.918002473008-0.7790911785092.162159301360.006651263331750.008803524062710.0207527419450.02836131600510.03957277523520.1960563631010.126714599218-0.354662760197-0.06943700418260.314295539883-0.02609604553350.03085161318180.392221453780.003272743422590.46398506328913.699200410114.1111668647-10.5843861994
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 481 through 724)AA481 - 7231 - 225
22(chain 'B' and resid 481 through 724)BB481 - 7241 - 244

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