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- PDB-8a17: Human PTPRM domains FN3-4, in spacegroup P3221 -

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Basic information

Entry
Database: PDB / ID: 8a17
TitleHuman PTPRM domains FN3-4, in spacegroup P3221
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 / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of endothelial cell proliferation / phosphatase activity / negative regulation of angiogenesis / protein dephosphorylation / protein-tyrosine-phosphatase ...retina layer formation / transmembrane receptor protein tyrosine phosphatase activity / negative regulation of endothelial cell migration / retinal ganglion cell axon guidance / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of endothelial cell proliferation / phosphatase activity / negative regulation of angiogenesis / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / adherens junction / neuron projection development / cell-cell junction / lamellipodium / response to xenobiotic stimulus / cadherin binding / 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 / 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. ...Receptor-type tyrosine-protein phosphatase mu, PTPase domain, repeat 1 / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsShamin, 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
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

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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
C: Receptor-type tyrosine-protein phosphatase mu
D: Receptor-type tyrosine-protein phosphatase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,24411
Polymers115,7894
Non-polymers4,4557
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)30,0633
Polymers28,9471
Non-polymers1,1162
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Receptor-type tyrosine-protein phosphatase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2513
Polymers28,9471
Non-polymers1,3032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Receptor-type tyrosine-protein phosphatase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2513
Polymers28,9471
Non-polymers1,3032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.531, 87.531, 311.235
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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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.: 4
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.: 3
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 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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
#5: 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.: 1 / 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
Has ligand of interestN

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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: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM ammonium nitrate and 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jan 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.08→77.89 Å / Num. obs: 26535 / % possible obs: 99.8 % / Redundancy: 10 % / Biso Wilson estimate: 91.59 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.1
Reflection shellResolution: 3.08→3.14 Å / Num. unique obs: 1199 / CC1/2: 0.391

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Processing

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

2v5y


Resolution: 3.09→75.8 Å / SU ML: 0.6004 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.8372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2897 1398 5.35 %
Rwork0.2434 24713 -
obs0.2458 26111 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.41 Å2
Refinement stepCycle: LAST / Resolution: 3.09→75.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7692 0 297 0 7989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01178204
X-RAY DIFFRACTIONf_angle_d1.359711189
X-RAY DIFFRACTIONf_chiral_restr0.07341307
X-RAY DIFFRACTIONf_plane_restr0.01141411
X-RAY DIFFRACTIONf_dihedral_angle_d12.85883061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.20.55391240.48592281X-RAY DIFFRACTION93.62
3.2-3.330.40681410.38892406X-RAY DIFFRACTION99.11
3.33-3.480.3531350.31422456X-RAY DIFFRACTION99.27
3.48-3.660.32971310.27262452X-RAY DIFFRACTION99.38
3.66-3.890.36141340.2962447X-RAY DIFFRACTION99.58
3.89-4.190.30191410.25752471X-RAY DIFFRACTION99.73
4.19-4.610.26511320.20272493X-RAY DIFFRACTION99.77
4.62-5.280.24661650.19192467X-RAY DIFFRACTION99.92
5.28-6.650.26751400.22662546X-RAY DIFFRACTION99.93
6.66-75.80.25741550.22092694X-RAY DIFFRACTION99.89
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)
10.397789454165-0.840703529560.009600951145880.1401149514790.409861075090.5989234803190.0007934156182540.0380214871669-0.192970001253-0.0129869193886-0.002488271523530.02333199346270.215168294811-0.2629331923247.90347470311E-50.843950634081-0.2201798955750.07578609267230.770687896374-0.04048253922380.916003581169-58.2458904476-4.60381801594-30.1066463107
20.628434761667-0.892824714738-0.08321092221850.6232835109080.06470565024791.394826841410.0614036944240.07413667369260.0141436875822-0.04020169602760.120682178253-0.0208089091675-0.6123762466610.466564365072-2.55006132261E-50.89298191915-0.261587771910.04441289760020.866074262045-0.008621405455190.8789816751-35.086667028832.7700643737-31.5151038518
30.562118873988-0.07457568449010.1750027061210.108711560975-0.02523858097621.10557771041-0.0285950448948-0.09152955417350.05997994859020.0591236054850.16642163388-0.00158724302173-0.508349674215-0.3477399008977.98605664962E-50.8888538548110.0318761994960.003456535388450.8710148215310.04111541908630.82553094628-54.558147111432.0204619424-16.0651633297
40.4394807895810.342095250739-0.3331754268050.1497097103030.4545803119380.809709413319-0.0985801043599-0.0546641303872-0.00235590057306-0.04495042543920.1505395529240.08099069378130.3286258455730.5096034460747.75587048407E-50.8639907301650.0005272573078280.07942012954290.787996689828-0.005080538221430.788050435661-34.3155476597-6.06715074713-24.7090124753
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 481 through 724)BF481 - 7241 - 244
22(chain 'C' and resid 481 through 724)CC481 - 7241 - 244
33(chain 'D' and resid 483 through 725)DD483 - 7251 - 243
44(chain 'A' and resid 481 through 724)AA481 - 7241 - 244

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