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- PDB-2i9b: Crystal structure of ATF-urokinase receptor complex -

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Basic information

Entry
Database: PDB / ID: 2i9b
TitleCrystal structure of ATF-urokinase receptor complex
Components
  • Urokinase plasminogen activator surface receptor
  • Urokinase-type plasminogen activator
KeywordsHYDROLASE / urokinase receptor / kringle domain / growth factor-like domain
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 / regulation of cell adhesion mediated by integrin / tertiary granule membrane / positive regulation of DNA binding / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / negative regulation of intrinsic apoptotic signaling pathway / 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 / positive regulation of protein phosphorylation / protein domain specific binding / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / signaling receptor binding / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / 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, 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 / Urokinase plasminogen activator surface receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLubkowski, J. / Barinka, C.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural basis of interaction between urokinase-type plasminogen activator and its receptor.
Authors: Barinka, C. / Parry, G. / Callahan, J. / Shaw, D.E. / Kuo, A. / Bdeir, K. / Cines, D.B. / Mazar, A. / Lubkowski, J.
History
DepositionSep 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.name
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 / 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 / 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.type / _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_unobs_or_zero_occ_atoms.label_asym_id / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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: Urokinase-type plasminogen activator
C: Urokinase-type plasminogen activator
D: Urokinase-type plasminogen activator
E: Urokinase plasminogen activator surface receptor
F: Urokinase plasminogen activator surface receptor
G: Urokinase plasminogen activator surface receptor
H: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,24814
Polymers190,0348
Non-polymers2,2146
Water93752
1
A: Urokinase-type plasminogen activator
E: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1914
Polymers47,5082
Non-polymers6832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-21 kcal/mol
Surface area20460 Å2
MethodPISA
2
B: Urokinase-type plasminogen activator
F: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1914
Polymers47,5082
Non-polymers6832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-20 kcal/mol
Surface area20460 Å2
MethodPISA
3
C: Urokinase-type plasminogen activator
G: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9333
Polymers47,5082
Non-polymers4241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-2 kcal/mol
Surface area19930 Å2
MethodPISA
4
D: Urokinase-type plasminogen activator
H: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9333
Polymers47,5082
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-9 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.914, 281.921, 62.811
Angle α, β, γ (deg.)90.00, 105.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F
14G
24H

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSALAALAAA11 - 13213 - 134
21CYSCYSALAALABB11 - 13213 - 134
12CYSCYSALAALACC11 - 13213 - 134
22CYSCYSALAALADD11 - 13213 - 134
13ARGARGASPASPEE2 - 2774 - 279
23ARGARGASPASPFF2 - 2774 - 279
14CYSCYSASPASPGG3 - 2775 - 279
24CYSCYSASPASPHH3 - 2775 - 279

NCS ensembles :
ID
1
2
3
4
DetailsThe biological unit is a heterodimer of ligand (ATF) and the receptor (uPAR). There are 4 biological units in the asymmetric unit.

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
Urokinase-type plasminogen activator


Mass: 16398.461 Da / Num. of mol.: 4 / Fragment: ATF, residues 21-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: pMT/BiP/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider's S2 cells / References: UniProt: P00749, u-plasminogen activator
#2: Protein
Urokinase plasminogen activator surface receptor / uPAR / U- PAR / Monocyte activation antigen Mo3 / CD87 antigen


Mass: 31109.963 Da / Num. of mol.: 4 / Fragment: UPAR, residues 23-299 / Mutation: N162Q, N172Q, N200Q, N233Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAUR, MO3, UPAR / Plasmid: pMT/BiP/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider's S2 cells / References: UniProt: Q03405

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Sugars , 2 types, 4 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-6)-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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-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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 54 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22.5% w/v PEG3350, 200 mM ammonium sulfate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Jul 7, 2005
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 47048 / Num. obs: 47048 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rsym value: 0.046 / Net I/σ(I): 17.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.44 / Num. unique all: 2636 / Rsym value: 0.206 / % possible all: 51.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YWH, 2I9A

1ywh

2i9a


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.899 / SU B: 30.164 / SU ML: 0.284 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26498 1911 4.1 %RANDOM
Rwork0.22194 ---
obs0.22372 44793 91.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.301 Å2
Baniso -1Baniso -2Baniso -3
1-3.8 Å20 Å22.52 Å2
2---3.9 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11696 0 144 52 11892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02111995
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.95816250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.87751490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45924.27548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.196151986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3441580
X-RAY DIFFRACTIONr_chiral_restr0.1310.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029084
X-RAY DIFFRACTIONr_nbd_refined0.2390.25471
X-RAY DIFFRACTIONr_nbtor_refined0.3140.38109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.3725
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.38
X-RAY DIFFRACTIONr_mcbond_it9.9381.57674
X-RAY DIFFRACTIONr_mcangle_it12.726211988
X-RAY DIFFRACTIONr_scbond_it15.95634804
X-RAY DIFFRACTIONr_scangle_it18.4744.54262
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A967tight positional0.040.05
2C967tight positional0.030.05
3E1992tight positional0.050.05
4G1854tight positional0.030.05
1A967tight thermal0.150.5
2C967tight thermal0.180.5
3E1992tight thermal0.120.5
4G1854tight thermal0.080.5
LS refinement shellResolution: 2.801→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 75 -
Rwork0.352 1656 -
obs--46.56 %
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)
14.5321-1.5472-0.6661.66580.14940.10320.0855-0.0807-0.0390.090.04610.1111-0.05080.0118-0.1317-0.1527-0.2478-0.08230.03220.0607-0.1433-23.9399141.25142.4007
20.72010.5421-1.66891.6928-1.45263.8976-0.08490.0294-0.10250.07590.03520.1016-0.0787-0.07510.0497-0.11070.1185-0.05550.0316-0.2248-0.1883-24.182239.063142.0771
30.52622.11550.4698.76891.67850.58040.1395-0.05120.01320.2927-0.1254-2.10580.1864-0.0228-0.01410.0345-0.0089-0.04790.0351-0.15331.00411.201187.884336.3959
40.14231.12820.32018.94362.53770.7201-0.137-0.00680.25-2.0903-0.1111-0.3017-0.0147-0.07160.24820.9351-0.1420.22480.0613-0.05040.063-9.055492.42699.8429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 13213 - 134
2X-RAY DIFFRACTION1EE3 - 2775 - 279
3X-RAY DIFFRACTION2BB11 - 13213 - 134
4X-RAY DIFFRACTION2FF3 - 2775 - 279
5X-RAY DIFFRACTION3CC11 - 13213 - 134
6X-RAY DIFFRACTION3GG3 - 2775 - 279
7X-RAY DIFFRACTION4DD11 - 13213 - 134
8X-RAY DIFFRACTION4HH3 - 2775 - 279

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