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- PDB-3laq: Structure-based engineering of species selectivity in the uPA-uPA... -

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Basic information

Entry
Database: PDB / ID: 3laq
TitleStructure-based engineering of species selectivity in the uPA-uPAR interaction
Components
  • Urokinase plasminogen activator surface receptorUrokinase receptor
  • Urokinase-type plasminogen activatorUrokinase
KeywordsHydrolase/Hydrolase Receptor / uPA / uPAR / ATF / suPAR / smuPAR / mATF / Disulfide bond / EGF-like domain / Hydrolase / Kringle / Plasminogen activation / Protease / Secreted / Serine protease / Zymogen / Cell membrane / Glycoprotein / GPI-anchor / Lipoprotein / Membrane / Receptor / Hydrolase-Hydrolase Receptor complex
Function / homology
Function and homology information


Attachment of GPI anchor to uPAR / Dissolution of Fibrin Clot / regulation of hepatocyte proliferation / positive regulation of homotypic cell-cell adhesion / skeletal muscle tissue regeneration / mesenchymal cell differentiation / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation ...Attachment of GPI anchor to uPAR / Dissolution of Fibrin Clot / regulation of hepatocyte proliferation / positive regulation of homotypic cell-cell adhesion / skeletal muscle tissue regeneration / mesenchymal cell differentiation / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / 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 / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / serine-type endopeptidase complex / smooth muscle cell migration / positive regulation of epidermal growth factor receptor signaling pathway / plasminogen activation / positive regulation of smooth muscle cell migration / regulation of cell adhesion mediated by integrin / positive regulation of release of cytochrome c from mitochondria / negative regulation of fibrinolysis / negative regulation of intrinsic apoptotic signaling pathway / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / Neutrophil degranulation / positive regulation of reactive oxygen species metabolic process / regulation of cell population proliferation / peptidase activity / angiogenesis / response to hypoxia / positive regulation of cell migration / positive regulation of protein phosphorylation / protein domain specific binding / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / cell surface / extracellular space / 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 / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CD59 / CD59 / Snake toxin-like superfamily ...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 / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CD59 / CD59 / Snake toxin-like superfamily / Laminin / Laminin / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Urokinase-type plasminogen activator / Urokinase plasminogen activator surface receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHuang, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure-based engineering of species selectivity in the interaction between urokinase and its receptor: implication for preclinical cancer therapy.
Authors: Lin, L. / Gardsvoll, H. / Huai, Q. / Huang, M. / Ploug, M.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
U: Urokinase plasminogen activator surface receptor
B: Urokinase-type plasminogen activator
V: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,55014
Polymers90,3374
Non-polymers2,21210
Water0
1
A: Urokinase-type plasminogen activator
U: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2757
Polymers45,1692
Non-polymers1,1065
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint1 kcal/mol
Surface area20340 Å2
MethodPISA
2
B: Urokinase-type plasminogen activator
V: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2757
Polymers45,1692
Non-polymers1,1065
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-1 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.421, 137.248, 65.785
Angle α, β, γ (deg.)90.00, 106.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Urokinase-type plasminogen activator / Urokinase / U-plasminogen activator / uPA / Urokinase-type plasminogen activator long chain A / Urokinase-type ...U-plasminogen activator / uPA / Urokinase-type plasminogen activator long chain A / Urokinase-type plasminogen activator short chain A / Urokinase-type plasminogen activator chain B


Mass: 14997.969 Da / Num. of mol.: 2 / Fragment: UNP residues 21-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plau / Plasmid: pMT / Production host: Drosophila (fruit flies) / Strain (production host): S2 cells / References: UniProt: P06869, u-plasminogen activator
#2: Protein Urokinase plasminogen activator surface receptor / Urokinase receptor / uPAR / U-PAR


Mass: 30170.777 Da / Num. of mol.: 2 / Fragment: UNP residues 24-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plaur / Plasmid: pMT / Production host: Drosophila (fruit flies) / Strain (production host): S2 cells / References: UniProt: P35456
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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

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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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 5-7 % (w/v) PEG 3350, 50 mM Bis-Tris at pH 5.5., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 17190 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.21 Å / % possible all: 54.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→44.74 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.771 / SU B: 70.075 / SU ML: 0.577 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.715 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.341 853 5.3 %RANDOM
Rwork0.231 ---
obs0.237 15297 93.3 %-
all-14272 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å2-0.77 Å2
2---2.84 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5895 0 140 0 6035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216203
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.81.9678419
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.275758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79423.741294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.30115984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2171552
X-RAY DIFFRACTIONr_chiral_restr0.1220.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5471.53803
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1226108
X-RAY DIFFRACTIONr_scbond_it1.73932400
X-RAY DIFFRACTIONr_scangle_it3.0924.52311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 48 -
Rwork0.256 760 -
obs--63.27 %
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)
11.41040.1777-0.31563.9989-0.55023.687-0.08790.1515-0.1565-0.37060.0181-0.23430.26970.11550.06980.1706-0.01460.05150.1635-0.08240.061821.322-3.06714.917
25.4312-0.76271.67685.4130.10417.04630.0236-0.64080.67190.60280.13420.269-0.6398-0.1852-0.15780.15850.0120.09830.0829-0.06860.14116.5641.98742.273
33.03150.76740.71123.3545-0.87332.31650.2566-0.0129-0.36420.205-0.185-0.39090.15740.263-0.07160.18150.102-0.02170.11170.00320.125437.16430.25832.406
43.2279-0.86020.12985.8826-3.92710.1037-0.1535-0.00560.4157-0.09460.29411.0512-0.7888-1.1924-0.14060.21750.0648-0.10620.1676-0.03420.35089.94437.36517.942
57.8211-1.1741-2.201911.06192.62075.0973-0.52670.08510.37430.21990.2665-1.2302-0.28051.33710.26020.7211-0.2960.32030.77760.01720.542541.2285.0533.956
65.5129-1.82222.041210.4136-0.16088.4932-0.2303-0.39840.02330.2414-0.31990.1398-1.26010.40780.55010.6272-0.107-0.20940.21540.0230.414548.40937.98352.253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 47
2X-RAY DIFFRACTION1U1 - 184
3X-RAY DIFFRACTION2A48 - 131
4X-RAY DIFFRACTION3B11 - 47
5X-RAY DIFFRACTION3V1 - 184
6X-RAY DIFFRACTION4B48 - 131
7X-RAY DIFFRACTION5U185 - 274
8X-RAY DIFFRACTION6V185 - 274

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