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- PDB-5lhr: The catalytic domain of murine urokinase-type plasminogen activat... -

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Basic information

Entry
Database: PDB / ID: 5lhr
TitleThe catalytic domain of murine urokinase-type plasminogen activator in complex with the active site binding inhibitory nanobody Nb22
Components
  • Camelid-Derived Antibody Fragment Nb22
  • Urokinase-type plasminogen activator
KeywordsHYDROLASE / Trypsin-like serine proteases / Nanobody / Inhibitor
Function / homology
Function and homology information


Dissolution of Fibrin Clot / regulation of hepatocyte proliferation / skeletal muscle tissue regeneration / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation ...Dissolution of Fibrin Clot / regulation of hepatocyte proliferation / skeletal muscle tissue regeneration / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / serine-type endopeptidase complex / smooth muscle cell migration / plasminogen activation / positive regulation of smooth muscle cell migration / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / Neutrophil degranulation / positive regulation of reactive oxygen species metabolic process / peptidase activity / regulation of cell population proliferation / angiogenesis / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / positive regulation of cell population proliferation / extracellular space
Similarity search - Function
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. ...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, 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 / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesMus musculus (house mouse)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKromann-Hansen, T. / Lange, E.L. / Sorensen, H.P. / Ghassabeh, G.H. / Huang, M. / Jensen, J.K. / Muyldermans, S. / Declerck, P.J. / Andreasen, P.A.
Funding support Denmark, China, 4items
OrganizationGrant numberCountry
Danish National Research Foundation26-331-6 Denmark
Lundbeck FoundationR83-A7826 Denmark
Carlsberg FoundationCF15-0814 Denmark
Natural Science Foundation of China31161130356, 31170707, 31370737 China
CitationJournal: Sci Rep / Year: 2017
Title: Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator.
Authors: Kromann-Hansen, T. / Louise Lange, E. / Peter Srensen, H. / Hassanzadeh-Ghassabeh, G. / Huang, M. / Jensen, J.K. / Muyldermans, S. / Declerck, P.J. / Komives, E.A. / Andreasen, P.A.
History
DepositionJul 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
B: Camelid-Derived Antibody Fragment Nb22


Theoretical massNumber of molelcules
Total (without water)42,8172
Polymers42,8172
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-3 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.095, 66.506, 57.027
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Urokinase-type plasminogen activator / uPA


Mass: 27554.158 Da / Num. of mol.: 1 / Mutation: C122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plau / Production host: Escherichia coli (E. coli) / References: UniProt: P06869, u-plasminogen activator
#2: Antibody Camelid-Derived Antibody Fragment Nb22


Mass: 15262.673 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Ammonium Acetate, 0.1 M Tris, 16 % w/v PEG 10.000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.3→32.47 Å / Num. obs: 14379 / % possible obs: 94.8 % / Redundancy: 4 % / CC1/2: 0.92 / Rmerge(I) obs: 0.107 / Net I/σ(I): 5.82
Reflection shellRmerge(I) obs: 0.4069

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→32.466 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 720 5.01 %
Rwork0.1876 --
obs0.1903 14379 89.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.299→32.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 0 173 2975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052872
X-RAY DIFFRACTIONf_angle_d1.1273888
X-RAY DIFFRACTIONf_dihedral_angle_d14.7251038
X-RAY DIFFRACTIONf_chiral_restr0.057407
X-RAY DIFFRACTIONf_plane_restr0.005502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2993-2.47680.31211500.2252857X-RAY DIFFRACTION95
2.4768-2.72590.29861550.21982931X-RAY DIFFRACTION96
2.7259-3.12010.28021550.19932944X-RAY DIFFRACTION97
3.1201-3.92990.22481040.18461983X-RAY DIFFRACTION93
3.9299-32.46940.17641560.15292944X-RAY DIFFRACTION96

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