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- PDB-6a8g: The crystal structure of muPAin-1-IG in complex with muPA-SPD at pH8.5 -

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Basic information

Entry
Database: PDB / ID: 6a8g
TitleThe crystal structure of muPAin-1-IG in complex with muPA-SPD at pH8.5
Components
  • Urokinase-type plasminogen activator chain B
  • muPAin-1-IG
KeywordsHYDROLASE INHIBITOR/HYDROLASE / Peptides inhibitor / muPA / serine protease / HYDROLASE / HYDROLASE INHIBITOR-HYDROLASE complex
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesMus musculus (house mouse)
Phage display vector pTDisp (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.53 Å
AuthorsWang, D. / Yang, Y.S. / Jiang, L.G. / Huang, M.D. / Li, J.Y. / Andreasen, P.A. / Xu, P. / Chen, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China21708043 China
National Natural Science Foundation of China81572944 China
National Natural Science Foundation of ChinaU1405229 China
CitationJournal: J.Med.Chem. / Year: 2019
Title: Suppression of Tumor Growth and Metastases by Targeted Intervention in Urokinase Activity with Cyclic Peptides.
Authors: Wang, D. / Yang, Y. / Jiang, L. / Wang, Y. / Li, J. / Andreasen, P.A. / Chen, Z. / Huang, M. / Xu, P.
History
DepositionJul 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
P: muPAin-1-IG
A: Urokinase-type plasminogen activator chain B
B: Urokinase-type plasminogen activator chain B
E: muPAin-1-IG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8989
Polymers57,4234
Non-polymers4755
Water61334
1
P: muPAin-1-IG
A: Urokinase-type plasminogen activator chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0916
Polymers28,7122
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-23 kcal/mol
Surface area11270 Å2
MethodPISA
2
B: Urokinase-type plasminogen activator chain B
E: muPAin-1-IG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8063
Polymers28,7122
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-20 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.010, 114.010, 103.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide muPAin-1-IG


Mass: 1157.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Phage display vector pTDisp (others)
#2: Protein Urokinase-type plasminogen activator chain B / uPA / muPA-SPD


Mass: 27554.158 Da / Num. of mol.: 2 / Mutation: C301A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plau
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P06869, u-plasminogen activator
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 80 mM Tris-HCl pH 8.5, 1.6 M NaH2PO4 and 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.53→71.39 Å / Num. obs: 26295 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 50.738 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.117 / Net I/σ(I): 16 / Num. measured all: 262704
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.53-2.5710.31.71318012750.4881.57599.9
6.87-71.428.8471266314310.0120.036100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
xia2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DVA

4dva


Resolution: 2.53→71.389 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 1372 5.23 %RANDOM
Rwork0.1906 ---
obs0.1934 26250 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.73 Å2 / Biso mean: 61.3391 Å2 / Biso min: 32.2 Å2
Refinement stepCycle: final / Resolution: 2.53→71.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 25 34 4064
Biso mean--82.55 67.33 -
Num. residues----513
Refinement TLS params.Method: refined / Origin x: 33.429 Å / Origin y: -34.866 Å / Origin z: 30.745 Å
111213212223313233
T0.4112 Å2-0.0269 Å2-0.0006 Å2-0.4535 Å2-0.0181 Å2--0.4259 Å2
L0.9222 °20.7009 °2-0.7579 °2-0.4519 °2-0.4092 °2--0.4359 °2
S0.2042 Å °-0.0715 Å °0.157 Å °0.1102 Å °-0.0837 Å °0.1016 Å °-0.1503 Å °0.052 Å °0.0006 Å °
Refinement TLS groupSelection details: all

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