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- PDB-4xsk: Structure of PAItrap, an uPA mutant -

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Basic information

Entry
Database: PDB / ID: 4xsk
TitleStructure of PAItrap, an uPA mutant
ComponentsUrokinase-type plasminogen activator
KeywordsBLOOD CLOTTING / antagonist / PAI-1 / uPA
Function / homology
Function and homology information


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 / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...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 / 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 / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
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. ...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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGong, L. / Proulle, V. / Hong, Z. / Lin, Z. / Liu, M. / Yuan, C. / Lin, L. / Furie, B. / Flaumenhaft, R. / Andreasen, P. ...Gong, L. / Proulle, V. / Hong, Z. / Lin, Z. / Liu, M. / Yuan, C. / Lin, L. / Furie, B. / Flaumenhaft, R. / Andreasen, P. / Furie, B. / Huang, M.
Funding support China, United States, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China31161130356 China
NFSC31370737 China
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL087203 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL095084 United States
CAS/SFEA International Partnership Program for Creative Research Teams China
NSF of Fujian Province2012J05071 China
CitationJournal: To Be Published
Title: Structure of PAItrap, an uPA mutant
Authors: Gong, L. / Proulle, V. / Hong, Z. / Lin, Z. / Liu, M. / Yuan, C. / Lin, L. / Furie, B. / Flaumenhaft, R. / Andreasen, P. / Furie, B. / Huang, M.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4327
Polymers27,7561
Non-polymers6776
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-18 kcal/mol
Surface area11310 Å2
Unit cell
Length a, b, c (Å)121.025, 121.025, 42.774
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Urokinase-type plasminogen activator / uPA


Mass: 27755.707 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 162-407 / Mutation: G37R, C122A, N145Q, S195A, R217L
Source method: isolated from a genetically manipulated source
Details: ...Details: IIGGEFTTIENQPWFAAIYRRHRRGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDAGGPLVCSLQGRMTLTGIVSWGLGCALKDKPGVYTRVSHFLPWIRSHTK
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: P00749, u-plasminogen activator
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.2 M ammonium sulfate, 5% PEG 400, 50 mM sodium citrate (pH 4.6)

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→34.94 Å / % possible obs: 99.82 % / Redundancy: 2 % / Net I/σ(I): 27
Reflection shell% possible all: 99.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H42

4h42


Resolution: 1.5→34.94 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.278 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20865 1869 5 %RANDOM
Rwork0.17394 ---
obs0.1757 35505 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.238 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å2-0 Å2
2---0.09 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 42 121 2108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192015
X-RAY DIFFRACTIONr_bond_other_d0.0020.021905
X-RAY DIFFRACTIONr_angle_refined_deg2.2191.9592687
X-RAY DIFFRACTIONr_angle_other_deg0.9834378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6575225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69723.21887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51815340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2981513
X-RAY DIFFRACTIONr_chiral_restr0.1310.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.81.489963
X-RAY DIFFRACTIONr_mcbond_other1.7971.487962
X-RAY DIFFRACTIONr_mcangle_it2.5512.1731167
X-RAY DIFFRACTIONr_mcangle_other2.552.1751168
X-RAY DIFFRACTIONr_scbond_it3.0931.9531052
X-RAY DIFFRACTIONr_scbond_other3.0921.9541053
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4592.7691521
X-RAY DIFFRACTIONr_long_range_B_refined5.98413.9262388
X-RAY DIFFRACTIONr_long_range_B_other5.98313.9342389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 155 -
Rwork0.222 2632 -
obs--99.61 %

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