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- PDB-3bt1: Structure of urokinase receptor, urokinase and vitronectin complex -

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Basic information

Entry
Database: PDB / ID: 3bt1
TitleStructure of urokinase receptor, urokinase and vitronectin complex
Components
  • Urokinase plasminogen activator surface receptorUrokinase receptor
  • Urokinase-type plasminogen activatorUrokinase
  • Vitronectin
KeywordsIMMUNE SYSTEM / protein-protein complex / Glycoprotein / GPI-anchor / Lipoprotein / Membrane / Receptor / Secreted / Blood coagulation / EGF-like domain / Fibrinolysis / Hydrolase / Kringle / Phosphoprotein / Plasminogen activation / Protease / Serine protease / Zymogen / Cell adhesion / Heparin-binding / Sulfation / Immunoglobulin domain
Function / homology
Function and homology information


urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / rough endoplasmic reticulum lumen / smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of homotypic cell-cell adhesion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / alphav-beta3 integrin-vitronectin complex / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion ...urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / rough endoplasmic reticulum lumen / smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of homotypic cell-cell adhesion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / alphav-beta3 integrin-vitronectin complex / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / scavenger receptor activity / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / negative regulation of endopeptidase activity / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of proteolysis / negative regulation of plasminogen activation / negative regulation of blood coagulation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / serine-type endopeptidase complex / Dissolution of Fibrin Clot / positive regulation of cell-substrate adhesion / Molecules associated with elastic fibres / cell adhesion mediated by integrin / smooth muscle cell migration / extracellular matrix structural constituent / positive regulation of epidermal growth factor receptor signaling pathway / Syndecan interactions / polysaccharide binding / extrinsic component of membrane / positive regulation of wound healing / plasminogen activation / positive regulation of smooth muscle cell migration / oligodendrocyte differentiation / endodermal cell differentiation / tertiary granule membrane / regulation of cell adhesion mediated by integrin / positive regulation of release of cytochrome c from mitochondria / protein polymerization / basement membrane / ECM proteoglycans / positive regulation of DNA binding / Integrin cell surface interactions / negative regulation of fibrinolysis / negative regulation of intrinsic apoptotic signaling pathway / specific granule membrane / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / collagen binding / extracellular matrix organization / cell-matrix adhesion / cell projection / liver regeneration / Regulation of Complement cascade / Golgi lumen / positive regulation of receptor-mediated endocytosis / chemotaxis / cell migration / positive regulation of peptidyl-tyrosine phosphorylation / blood coagulation / integrin binding / signaling receptor activity / heparin binding / regulation of cell population proliferation / positive regulation of protein binding / collagen-containing extracellular matrix / blood microparticle / response to hypoxia / cell adhesion / positive regulation of cell migration / immune response / positive regulation of protein phosphorylation / protein domain specific binding / external side of plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / endoplasmic reticulum / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / 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 / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain ...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 / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CD59 / CD59 / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / 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, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Vitronectin / Urokinase plasminogen activator surface receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuang, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes
Authors: Huai, Q. / Zhou, A. / Lin, L. / Mazar, A.P. / Parry, G.C. / Callahan, J. / Shaw, D.E. / Furie, B. / Furie, B.C. / Huang, M.
History
DepositionDec 27, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 11, 2019Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_validate_close_contact ...database_PDB_caveat / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.3Dec 18, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 2.1Nov 1, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,5636
Polymers51,5343
Non-polymers1,0293
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint1 kcal/mol
Surface area22940 Å2
Unit cell
Length a, b, c (Å)97.353, 105.187, 55.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Urokinase-type plasminogen activator / Urokinase / uPA / U-plasminogen activator


Mass: 15359.318 Da / Num. of mol.: 1
Fragment: urokinase amino terminal fragment, Urokinase-type plasminogen activator long chain A, UNP residues 21-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: PMT/BIP / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 CELLS / References: UniProt: P00749
#2: Protein/peptide Vitronectin / / Serum-spreading factor / S-protein / V75


Mass: 4573.103 Da / Num. of mol.: 1 / Fragment: sometomedin-B domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VTN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04004
#3: Protein Urokinase plasminogen activator surface receptor / Urokinase receptor / uPAR / U-PAR / Monocyte activation antigen Mo3 / CD87 antigen


Mass: 31601.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAUR, MO3, UPAR / Plasmid: PMT/BIP / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 CELLS / References: UniProt: Q03405
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 295 K / Method: microdialysis / pH: 7.5
Details: 12% PEG 3350, 50mM HEPES pH 7.5, MICRODIALYSIS, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 14540 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 82 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 33.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.803 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FD6

2fd6


Resolution: 2.8→27.68 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.889 / SU B: 43.465 / SU ML: 0.374 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.308 726 5 %RANDOM
Rwork0.241 ---
obs0.244 13778 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.05 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2---3.25 Å20 Å2
3---2.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→27.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 67 0 3461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213560
X-RAY DIFFRACTIONr_bond_other_d0.0020.022473
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.9624821
X-RAY DIFFRACTIONr_angle_other_deg1.0483.0165921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4645434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37124.302172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.24815595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.561525
X-RAY DIFFRACTIONr_chiral_restr0.1020.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023950
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02686
X-RAY DIFFRACTIONr_nbd_refined0.2660.21061
X-RAY DIFFRACTIONr_nbd_other0.2210.22877
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21752
X-RAY DIFFRACTIONr_nbtor_other0.10.22006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1630.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0640.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7461.52697
X-RAY DIFFRACTIONr_mcbond_other0.1051.5909
X-RAY DIFFRACTIONr_mcangle_it0.95823478
X-RAY DIFFRACTIONr_scbond_it1.35631573
X-RAY DIFFRACTIONr_scangle_it2.1544.51343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.598 54 -
Rwork0.399 1005 -
obs--100 %

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