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- PDB-4k24: Structure of anti-uPAR Fab ATN-658 in complex with uPAR -

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Basic information

Entry
Database: PDB / ID: 4k24
TitleStructure of anti-uPAR Fab ATN-658 in complex with uPAR
Components
  • (anti-uPAR antibody, ...) x 2
  • Urokinase plasminogen activator surface receptorUrokinase receptor
  • Urokinase-type plasminogen activatorUrokinase
  • Vitronectin
KeywordsIMMUNE SYSTEM
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 / negative regulation of blood coagulation / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / scavenger receptor activity / 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 / regulation of smooth muscle cell migration / regulation of signaling receptor activity / extracellular matrix binding / serine-type endopeptidase complex / positive regulation of vascular endothelial growth factor receptor signaling pathway / Dissolution of Fibrin Clot / positive regulation of cell-substrate adhesion / Molecules associated with elastic fibres / cell adhesion mediated by integrin / smooth muscle cell migration / positive regulation of epidermal growth factor receptor signaling pathway / extracellular matrix structural constituent / Syndecan interactions / extrinsic component of membrane / polysaccharide binding / positive regulation of wound healing / plasminogen activation / positive regulation of smooth muscle cell migration / oligodendrocyte differentiation / endodermal cell differentiation / positive regulation of release of cytochrome c from mitochondria / tertiary granule membrane / regulation of cell adhesion mediated by integrin / 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 / collagen binding / fibrinolysis / extracellular matrix organization / cell-matrix adhesion / cell projection / liver regeneration / Regulation of Complement cascade / Golgi lumen / positive regulation of receptor-mediated endocytosis / chemotaxis / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / 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 / endoplasmic reticulum lumen / external side of plasma membrane / 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. / 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 / 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 / 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
Similarity search - Domain/homology
alpha-D-mannopyranose / Urokinase-type plasminogen activator / Vitronectin / Urokinase plasminogen activator surface receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsHuang, M.D. / Xu, X. / Yuan, C.
CitationJournal: Plos One / Year: 2014
Title: Identification of a New Epitope in uPAR as a Target for the Cancer Therapeutic Monoclonal Antibody ATN-658, a Structural Homolog of the uPAR Binding Integrin CD11b ( alpha M)
Authors: Xu, X. / Cai, Y. / Wei, Y. / Donate, F. / Juarez, J. / Parry, G. / Chen, L. / Meehan, E.J. / Ahn, R.W. / Ugolkov, A. / Dubrovskyi, O. / O'halloran, T.V. / Huang, M. / Mazar, A.P.
History
DepositionApr 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Data collection
Revision 1.2Dec 11, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: pdbx_nonpoly_scheme / pdbx_struct_assembly ...pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_biol / struct_conn / struct_ref_seq_dif
Item: _pdbx_nonpoly_scheme.ndb_seq_num / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.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_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 8, 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
H: anti-uPAR antibody, heavy chain
L: anti-uPAR antibody, light chain
U: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4239
Polymers100,1735
Non-polymers1,2504
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-29 kcal/mol
Surface area41430 Å2
Unit cell
Length a, b, c (Å)164.659, 164.659, 391.582
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 2 types, 2 molecules AU

#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: 15359.318 Da / Num. of mol.: 1 / Fragment: 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): Schneider 2 / References: UniProt: P00749, u-plasminogen activator
#5: Protein Urokinase plasminogen activator surface receptor / Urokinase receptor / U-PAR / uPAR / Monocyte activation antigen Mo3


Mass: 31601.479 Da / Num. of mol.: 1 / Fragment: UNP residues 23-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MO3, PLAUR, UPAR / Plasmid: pMT/Bip / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 / References: UniProt: Q03405

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Protein/peptide , 1 types, 1 molecules B

#2: Protein/peptide Vitronectin / / VN / S-protein / Serum-spreading factor / V75 / Vitronectin V65 subunit / Vitronectin V10 subunit / ...VN / S-protein / Serum-spreading factor / V75 / Vitronectin V65 subunit / Vitronectin V10 subunit / Somatomedin-B


Mass: 4573.103 Da / Num. of mol.: 1 / Fragment: UNP residues 21-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VTN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04004

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Antibody , 2 types, 2 molecules HL

#3: Antibody anti-uPAR antibody, heavy chain


Mass: 24482.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody anti-uPAR antibody, light chain


Mass: 24156.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 3 types, 4 molecules

#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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: 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
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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Details

Sequence detailsA SEQUENCE DATABASE REFERENCE FOR ENTITY 3 AND 4 DOES NOT CURRENTLY EXIST.

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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: 5.1 Å3/Da / Density % sol: 75.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 55%(v/v) Tacsimate, 2%(v/v) 2-methyl-1,3-propanediol, vapor diffusion, sitting drop, temperature 295K

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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: Jan 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 4.5→27 Å / Num. obs: 12451 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
4.5-4.664.50.8411100
4.66-4.854.60.6281100
4.85-5.064.50.4891100
5.06-5.334.50.4441100
5.33-5.664.50.414199.9
5.66-6.094.50.301199.8
6.09-6.74.50.233199.9
6.7-7.654.40.151199.7
7.65-9.564.10.081199.1
9.56-273.70.053198.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BT2(chain A, B, U), 4K23(chain H, L)

3bt2

4k23


Resolution: 4.5→26.902 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.51 / σ(F): 1.34 / Phase error: 30.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 602 4.84 %
Rwork0.2174 --
obs0.22 12432 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 284.9089 Å2
Baniso -1Baniso -2Baniso -3
1-13.44 Å20 Å2-0 Å2
2--13.44 Å2-0 Å2
3----26.88 Å2
Refinement stepCycle: LAST / Resolution: 4.5→26.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6690 0 81 0 6771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136948
X-RAY DIFFRACTIONf_angle_d2.0179371
X-RAY DIFFRACTIONf_dihedral_angle_d20.4142544
X-RAY DIFFRACTIONf_chiral_restr0.1321034
X-RAY DIFFRACTIONf_plane_restr0.0081208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5-4.93430.27921580.25352880X-RAY DIFFRACTION99
4.9343-5.64250.29911550.24052940X-RAY DIFFRACTION100
5.6425-7.08740.27621390.22462971X-RAY DIFFRACTION100
7.0874-26.90290.26661500.23039X-RAY DIFFRACTION99
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)
15.36270.97411.6251-0.6562.99483.6246-0.0501-0.5488-0.6942-0.68070.0290.11280.7341-0.61330.3412.1128-0.33010.08291.97230.01542.425830.669729.690552.7353
27.1548-1.24-8.11710.46581.35749.2023-2.6771-3.16271.35680.48390.6504-0.06120.63220.1252.22042.3569-0.0374-0.31733.44220.10992.453516.811325.70882.174
31.8017-1.69050.07820.0348-1.59744.8272-0.1036-0.03060.4133-0.23360.7136-0.137-0.5576-0.3305-0.60511.7406-0.18270.1032.083-0.20582.3148-2.26629.346154.0831
4-1.0037-1.16630.346-0.00410.33749.93940.72671.35860.7132-0.4628-0.5035-0.66770.5711-0.19930.20342.4315-0.22130.19443.42160.28332.4659-41.911913.135316.8476
51.169-0.88384.41721.5560.36482.7252-1.38381.31980.6265-1.244-0.18140.9262-2.07661.0930.2173.0456-0.2477-0.22113.62720.09052.6696-46.010629.53629.3293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'U'
4X-RAY DIFFRACTION4chain 'H'
5X-RAY DIFFRACTION5chain 'L'

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