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- PDB-2fd6: Structure of Human Urokinase Plasminogen Activator in Complex wit... -

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Entry
Database: PDB / ID: 2fd6
TitleStructure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A
Components
  • H chain of Fab of ATN-615 anti-uPAR antibody
  • L chain of Fab of ATN-615 anti-uPAR antibody
  • Urokinase plasminogen activator surface receptorUrokinase receptor
  • Urokinase-type plasminogen activatorUrokinase
KeywordsIMMUNE SYSTEM / HYDROLASE / uPAR / ATF / ATN-615 antibody / Fab / ternary complex
Function / homology
Function and homology information


urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / positive regulation of homotypic cell-cell adhesion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing ...urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / positive regulation of homotypic cell-cell adhesion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of proteolysis / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / positive regulation of epidermal growth factor receptor signaling pathway / extrinsic component of membrane / plasminogen activation / positive regulation of release of cytochrome c from mitochondria / tertiary granule membrane / regulation of cell adhesion mediated by integrin / positive regulation of DNA binding / negative regulation of fibrinolysis / negative regulation of intrinsic apoptotic signaling pathway / specific granule membrane / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / cell projection / chemotaxis / blood coagulation / signaling receptor activity / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / immune response / positive regulation of protein phosphorylation / protein domain specific binding / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / metal ion 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 / 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set 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 / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-ETHOXYETHANOL / 2-acetamido-2-deoxy-alpha-D-glucopyranose / TRIETHYLENE GLYCOL / Urokinase-type plasminogen activator / Urokinase plasminogen activator surface receptor / : / ENSMUSG00000076577 protein / V165-D-J-C mu protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHuang, M. / Huai, Q. / Li, Y.
CitationJournal: Science / Year: 2006
Title: Structure of human urokinase plasminogen activator in complex with its receptor
Authors: Huai, Q. / Mazar, A.P. / Kuo, A. / Parry, G.C. / Shaw, D.E. / Callahan, J. / Li, Y. / Yuan, C. / Bian, C. / Chen, L. / Furie, B. / Furie, B.C. / Cines, D.B. / Huang, M.
History
DepositionDec 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 18, 2012Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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
Remark 999SEQUENCE The aminoacid sequence database reference is currently not available for Fab atn-615 anti- ...SEQUENCE The aminoacid sequence database reference is currently not available for Fab atn-615 anti-uPAR antibody, light and heavy chains

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
L: L chain of Fab of ATN-615 anti-uPAR antibody
H: H chain of Fab of ATN-615 anti-uPAR antibody
U: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,83215
Polymers90,9844
Non-polymers1,84811
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-10 kcal/mol
Surface area36920 Å2
MethodPISA
2
A: Urokinase-type plasminogen activator
U: Urokinase plasminogen activator surface receptor
hetero molecules

L: L chain of Fab of ATN-615 anti-uPAR antibody
H: H chain of Fab of ATN-615 anti-uPAR antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,83215
Polymers90,9844
Non-polymers1,84811
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area8480 Å2
ΔGint-18 kcal/mol
Surface area38220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.792, 86.805, 124.690
Angle α, β, γ (deg.)90.00, 94.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AU

#1: Protein Urokinase-type plasminogen activator / Urokinase


Mass: 13892.803 Da / Num. of mol.: 1 / Fragment: Amino terminal residues 31-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Drosophila / Cell line (production host): S2 cells / Production host: Drosophila (fruit flies) / References: UniProt: P00749, u-plasminogen activator
#4: Protein Urokinase plasminogen activator surface receptor / Urokinase receptor / uPAR / U-PAR / Monocyte activation antigen Mo3 / CD87 antigen


Mass: 30668.418 Da / Num. of mol.: 1 / Fragment: residues 23-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Drosophila / Cell line (production host): S2 cells / Production host: Drosophila (fruit flies) / References: UniProt: Q03405

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Antibody , 2 types, 2 molecules LH

#2: Antibody L chain of Fab of ATN-615 anti-uPAR antibody


Mass: 23437.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Secretion: ascite liquid / References: UniProt: Q52L64
#3: Antibody H chain of Fab of ATN-615 anti-uPAR antibody


Mass: 22984.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Secretion: ascite liquid / References: UniProt: Q4V9V8, UniProt: Q924Q0*PLUS

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Sugars , 3 types, 3 molecules

#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#11: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 344 molecules

#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#12: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 6.5
Details: 4% PEG4000, 5% ethylene glycol, 5% methanol, 0.05% sodium azide, 50 mM cacodylate, pH 6.5, MICRODIALYSIS, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11
SYNCHROTRONNSLS X2521
SYNCHROTRONNSLS X12C31
SYNCHROTRONAPS 17-ID4
Detector
TypeIDDetectorDate
MARRESEARCH1CCDApr 9, 2005
2CCD
3CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.85→41.36 Å / Num. obs: 86852 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.1
Reflection shellResolution: 1.85→2.08 Å / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 1.97 / % possible all: 77.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FAT

2fat


Resolution: 1.9→41.36 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1755432.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 4228 5.1 %RANDOM
Rwork0.239 ---
all0.239 86852 --
obs0.239 83101 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.429597 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-3.7 Å2
2--4.95 Å20 Å2
3----4.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6139 0 125 336 6600
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 559 5 %
Rwork0.403 10624 -
obs--77.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2temp.dummy
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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