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- PDB-1oc0: plasminogen activator inhibitor-1 complex with somatomedin B doma... -

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Basic information

Entry
Database: PDB / ID: 1oc0
Titleplasminogen activator inhibitor-1 complex with somatomedin B domain of vitronectin
Components
  • PLASMINOGEN ACTIVATOR INHIBITOR-1
  • VITRONECTIN
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / SERINE PROTEASE INHIBITOR-COMPLEX / SERPIN / PROTEINASE INHIBITOR / FIBRINOLYSIS / CELL MIGRATION / PLASMINOGEN ACTIVATION / HEPARIN-BINDING / CELL ADHESION
Function / homology
Function and homology information


positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / negative regulation of smooth muscle cell migration / peptidase inhibitor complex / negative regulation of vascular wound healing / negative regulation of wound healing / alphav-beta3 integrin-vitronectin complex ...positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / negative regulation of smooth muscle cell migration / peptidase inhibitor complex / negative regulation of vascular wound healing / negative regulation of wound healing / alphav-beta3 integrin-vitronectin complex / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / scavenger receptor activity / negative regulation of endopeptidase activity / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / negative regulation of blood coagulation / positive regulation of monocyte chemotaxis / regulation of signaling receptor activity / positive regulation of vascular endothelial growth factor receptor signaling pathway / extracellular matrix binding / Dissolution of Fibrin Clot / positive regulation of cell-substrate adhesion / Molecules associated with elastic fibres / extracellular matrix structural constituent / cell adhesion mediated by integrin / polysaccharide binding / Syndecan interactions / positive regulation of wound healing / positive regulation of smooth muscle cell migration / endodermal cell differentiation / oligodendrocyte differentiation / replicative senescence / basement membrane / protein polymerization / ECM proteoglycans / positive regulation of blood coagulation / Integrin cell surface interactions / negative regulation of fibrinolysis / regulation of cell adhesion / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / serine protease inhibitor complex / fibrinolysis / collagen binding / extracellular matrix organization / cell-matrix adhesion / BMAL1:CLOCK,NPAS2 activates circadian gene expression / platelet alpha granule lumen / negative regulation of cell migration / Regulation of Complement cascade / positive regulation of interleukin-8 production / liver regeneration / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / serine-type endopeptidase inhibitor activity / positive regulation of receptor-mediated endocytosis / Golgi lumen / positive regulation of inflammatory response / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / cell migration / positive regulation of protein binding / Platelet degranulation / heparin binding / cellular response to lipopolysaccharide / protease binding / angiogenesis / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / blood microparticle / cell adhesion / immune response / intracellular membrane-bounded organelle / signaling receptor binding / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / 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. / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 ...: / 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. / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Vitronectin / Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsRead, R.J. / Zhou, A. / Huntington, J.A. / Pannu, N.S. / Carrell, R.W.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: How Vitronectin Binds Pai-1 to Modulate Fibrinolysis and Cell Migration
Authors: Zhou, A. / Huntington, J.A. / Pannu, N.S. / Carrell, R.W. / Read, R.J.
History
DepositionFeb 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASMINOGEN ACTIVATOR INHIBITOR-1
B: VITRONECTIN


Theoretical massNumber of molelcules
Total (without water)48,6072
Polymers48,6072
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.501, 90.087, 100.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PLASMINOGEN ACTIVATOR INHIBITOR-1 / ENDOTHELIAL PLASMINOGEN ACTIVATOR INHIBITOR / PAI-1 / PAI


Mass: 42782.023 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05121
#2: Protein VITRONECTIN / SERUM SPREADING FACTOR / S-PROTEIN / S75


Mass: 5824.493 Da / Num. of mol.: 1 / Fragment: SOMATOMEDIN B, RESIDUES 20-70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: OBTAINED BY CNBR CLEAVAGE OF FUSION PROTEIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AD494(DE3) / References: UniProt: P04004
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION ASN 173 HIS, LYS 177 THR, GLN 342 LEU AND MET 377 ILE IN CHAIN A. MOL_ID 1: ...ENGINEERED MUTATION ASN 173 HIS, LYS 177 THR, GLN 342 LEU AND MET 377 ILE IN CHAIN A. MOL_ID 1: INHIBITOR FOR TISSUE PLASMINOGEN ACTIVATOR (TPA), PROTEIN C AND UROKINASE. RAPID INTERACTION WITH TPA COULD ACT AS A CONTROL POINT IN THE REGULATION OF FIBRINOLYSIS. HIGH CONCENTRATIONS IMPLICATED IN HUMAN THROMBOEMBOLIC DISEASE. MOL_ID 2: SOMATOMEDIN B IS A GROWTH HORMONE-DEPENDENT SERUM FACTOR THAT DISPLAYS PROTEASE-INHIBITING ACTIVITY.
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.4
Details: 10MM NAOAC, 50MM NACL, 2-9% PEG12000,25% PEG400, 50MM HEPES, PH 7.4
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13 mg/mlprotein1drop
210 mMsodium acetate1drop
350 mM1dropNaCl
42-9 %(w/v)PEG120001reservoir
550 mMHEPES1reservoirpH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorType: APS / Detector: CCD / Date: Apr 15, 2002 / Details: FOCUSING MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.28→45 Å / Num. obs: 20251 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 45.806 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 7.9
Reflection shellResolution: 2.28→2.37 Å / Redundancy: 7 % / Rmerge(I) obs: 0.733 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.28 Å / Lowest resolution: 45 Å / % possible obs: 99.95 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.112
Reflection shell
*PLUS
% possible obs: 99.95 % / Redundancy: 7 % / Num. unique obs: 2204 / Rmerge(I) obs: 0.733

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B3K

1b3k


Resolution: 2.28→45 Å / SU B: 6.866 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.242 / Details: TLS GROUPS USED FOR PAI-1 AND SOMATOMEDIN B
RfactorNum. reflection% reflectionSelection details
Rfree0.252 989 4.9 %RANDOM
Rwork0.196 ---
obs0.198 20251 99.95 %-
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2---0.76 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.28→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 0 137 3324
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.343 / Rfactor Rwork: 0.272

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