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- PDB-6aex: Crystal structure of unoccupied murine uPAR -

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Basic information

Entry
Database: PDB / ID: 6aex
TitleCrystal structure of unoccupied murine uPAR
ComponentsUrokinase plasminogen activator surface receptorUrokinase receptor
KeywordsCELL INVASION / uPAR / TFPDs
Function / homology
Function and homology information


Attachment of GPI anchor to uPAR / Dissolution of Fibrin Clot / positive regulation of homotypic cell-cell adhesion / mesenchymal cell differentiation / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / epithelial cell differentiation involved in prostate gland development / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / serine-type endopeptidase complex ...Attachment of GPI anchor to uPAR / Dissolution of Fibrin Clot / positive regulation of homotypic cell-cell adhesion / mesenchymal cell differentiation / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / epithelial cell differentiation involved in prostate gland development / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / serine-type endopeptidase complex / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of release of cytochrome c from mitochondria / regulation of cell adhesion / negative regulation of intrinsic apoptotic signaling pathway / Neutrophil degranulation / positive regulation of protein phosphorylation / protein domain specific binding / external side of plasma membrane / signaling receptor binding / negative regulation of apoptotic process / enzyme binding / cell surface / extracellular region / plasma membrane
Similarity search - Function
CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. / Ly-6 antigen / uPA receptor -like domain / u-PAR/Ly-6 domain / Ly-6 antigen/uPA receptor-like / Snake toxin-like superfamily
Similarity search - Domain/homology
Urokinase plasminogen activator surface receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 Å
AuthorsMin, L. / Huang, M.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370737 China
National Natural Science Foundation of China31400637 China
National Natural Science Foundation of China31570745 China
National Natural Science Foundation of China31670739 China
CitationJournal: Febs Lett. / Year: 2019
Title: Crystal structure of the unoccupied murine urokinase-type plasminogen activator receptor (uPAR) reveals a tightly packed DII-DIII unit.
Authors: Liu, M. / Lin, L. / Hoyer-Hansen, G. / Ploug, M. / Li, H. / Jiang, L. / Yuan, C. / Li, J. / Huang, M.
History
DepositionAug 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3922
Polymers30,1711
Non-polymers2211
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint2 kcal/mol
Surface area9040 Å2
Unit cell
Length a, b, c (Å)83.820, 83.820, 81.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Urokinase plasminogen activator surface receptor / Urokinase receptor / uPAR


Mass: 30170.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plaur / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P35456
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.4 / Details: 50mM Tris.Cl, 3M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.04 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.393→37.261 Å / Num. obs: 11915 / % possible obs: 99.74 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 45.5
Reflection shellResolution: 2.393→2.479 Å / Rmerge(I) obs: 0.786 / Num. unique obs: 585

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LAQ

3laq


Resolution: 2.393→37.261 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 636 5.34 %
Rwork0.1948 --
obs0.1976 11910 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.393→37.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 14 27 1261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081270
X-RAY DIFFRACTIONf_angle_d1.0111728
X-RAY DIFFRACTIONf_dihedral_angle_d7.525739
X-RAY DIFFRACTIONf_chiral_restr0.053187
X-RAY DIFFRACTIONf_plane_restr0.005227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3933-2.57810.29061160.25122190X-RAY DIFFRACTION100
2.5781-2.83750.25261020.21442239X-RAY DIFFRACTION100
2.8375-3.24780.2821510.21652209X-RAY DIFFRACTION100
3.2478-4.09110.24811200.18652266X-RAY DIFFRACTION100
4.0911-37.26560.22071470.17782370X-RAY DIFFRACTION100
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)
14.16250.32864.5953.48322.92616.9305-1.5436-1.05010.80481.5421-1.133-0.11370.42892.5941.19441.3021-0.2089-0.17771.8050.13130.946860.842127.782647.6551
21.0861-1.51520.33123.42930.0032.8436-0.2645-0.0764-0.4918-0.1886-0.15210.21710.4077-0.1260.36880.3487-0.02020.04510.45880.10180.380559.835626.164431.4866
38.25357.8971.90047.54041.66044.4454-0.1145-1.71953.51150.58560.6425-1.7157-0.64111.7672-0.38180.5351-0.1219-0.25061.021-0.15151.196574.377632.893542.3537
41.5963-1.86961.12796.20590.4693.3710.4646-0.4819-0.2597-0.0059-0.45510.4492-0.47140.22730.20360.2696-0.0410.02050.5120.03520.341665.946828.184531.196
57.02721.2797-2.47831.90530.08065.63950.3918-0.08780.7563-0.3876-0.9175-0.9738-0.3584-0.08340.53730.54830.0563-0.07810.76510.19770.661272.816829.36727.5488
65.4633.86641.19788.4678-1.24621.1694-1.2384-2.35260.9313-2.2574-0.60270.5314-1.22090.13940.83721.2609-0.2419-0.12151.44460.2081.705974.367637.775134.3606
70.06970.1096-0.45780.1755-0.79173.4553-0.0879-1.13570.56410.29920.3565-1.5098-1.83991.192-0.15050.6137-0.11610.02070.8010.01081.231478.77832.464736.7488
82.20851.962-0.8342.8278-0.42571.5158-0.3987-0.5768-1.0685-0.02340.1849-0.46260.09260.3493-0.00020.4220.09560.03330.65510.19410.551763.935719.955837.0491
95.04520.97450.12685.67590.03798.83840.65060.57070.3353-1.4280.1546-0.9549-0.42030.7617-0.95760.5647-0.03210.18390.4128-0.03880.662568.094943.81755.688
103.4668-1.48940.30265.42163.20172.34-0.39780.35330.64752.41890.61893.2775-0.5393-0.01080.00711.08590.00780.3120.5420.15751.016161.269551.888420.0068
116.3607-1.1063-2.51683.59070.50688.5464-1.2188-1.43330.81170.1979-0.33570.1154-0.75390.62250.94590.8530.1498-0.06520.97880.20141.609854.902650.899714.7584
123.1656-2.8536-3.70763.99811.98656.8397-0.4614-0.8895-0.54240.21270.2326-0.71240.2830.72950.18780.59460.11310.13120.35170.04190.690169.059247.17927.3901
133.8751.3702-0.10822.0895-2.02893.25070.18091.8853-1.7071-0.62460.3559-1.4042-0.00032.0395-0.24130.7401-0.01390.11971.07270.2091.24574.709538.01887.921
143.69720.4568-1.08651.4644-0.61066.77410.1386-0.46540.20310.76540.14580.4192-2.46510.4376-0.31160.97520.02120.12470.3614-0.02360.645663.479841.860624.6322
152.27820.8932-2.34746.28660.78279.1465-0.6409-0.42680.95750.0131-0.01740.51090.08610.86010.37250.53450.03770.0280.3471-0.02340.553964.526144.642219.2132
160.2293-0.4295-0.78250.78081.43232.555-1.405-1.51610.50310.98090.0096-0.95941.0510.22091.35380.74770.27520.02310.71610.07361.050172.61333.471815.0855
177.6263-0.0878-4.75254.5627-0.30543.69320.5895-1.0350.45480.24290.12460.0578-1.23060.8316-0.73990.34440.0020.01630.32410.0110.515361.635833.328430.7052
181.88460.6334-0.27561.2344-0.63759.78-0.08880.0278-0.1281-0.16350.1498-0.34990.11870.00440.16510.53570.00820.06130.3240.00210.464.34435.87416.8219
191.92461.1268-0.95213.3157-0.7293.35030.3692-0.256-0.00140.3126-0.13250.1719-0.6422-0.0491-0.24980.34350.0450.08810.33970.07140.42855.544433.744222.0691
205.53885.73843.86786.89665.28596.71260.8501-0.62690.3141-0.1862-0.582-1.6768-0.7338-0.4488-0.11980.5206-0.01770.08680.60070.04730.772361.513329.391540.0867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain U and resid 203:209)
2X-RAY DIFFRACTION2(chain U and resid 210:223)
3X-RAY DIFFRACTION3(chain U and resid 224:235)
4X-RAY DIFFRACTION4(chain U and resid 236:244)
5X-RAY DIFFRACTION5(chain U and resid 245:250)
6X-RAY DIFFRACTION6(chain U and resid 251:256)
7X-RAY DIFFRACTION7(chain U and resid 257:262)
8X-RAY DIFFRACTION8(chain U and resid 263:274)
9X-RAY DIFFRACTION9(chain U and resid 92:98)
10X-RAY DIFFRACTION10(chain U and resid 99:106)
11X-RAY DIFFRACTION11(chain U and resid 107:111)
12X-RAY DIFFRACTION12(chain U and resid 112:117)
13X-RAY DIFFRACTION13(chain U and resid 118:122)
14X-RAY DIFFRACTION14(chain U and resid 123:139)
15X-RAY DIFFRACTION15(chain U and resid 140:145)
16X-RAY DIFFRACTION16(chain U and resid 146:152)
17X-RAY DIFFRACTION17(chain U and resid 153:162)
18X-RAY DIFFRACTION18(chain U and resid 163:172)
19X-RAY DIFFRACTION19(chain U and resid 173:191)
20X-RAY DIFFRACTION20(chain U and resid 192:197)

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