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Basic information

Entry
Database: PDB / ID: 6i8s
TitleDiscovery and characterisation of an antibody that selectively modulates the inhibitory activity of plasminogen activator inhibitor-1
Components
  • HEAVY CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
  • LIGHT CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
  • Plasminogen activator inhibitor 1
KeywordsBLOOD CLOTTING / SERPIN / PLASMINOGEN ACTIVATOR INHIBITOR-1 / PAI-1 / ANTIBODY / FAB
Function / homology
Function and homology information


positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of coagulation / negative regulation of smooth muscle cell migration / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation ...positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of coagulation / negative regulation of smooth muscle cell migration / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / regulation of signaling receptor activity / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / positive regulation of monocyte chemotaxis / replicative senescence / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / ECM proteoglycans / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / serine protease inhibitor complex / fibrinolysis / negative regulation of proteolysis / BMAL1:CLOCK,NPAS2 activates circadian expression / platelet alpha granule lumen / negative regulation of cell migration / positive regulation of interleukin-8 production / serine-type endopeptidase inhibitor activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / positive regulation of inflammatory response / Platelet degranulation / : / cellular response to lipopolysaccharide / protease binding / angiogenesis / defense response to Gram-negative bacterium / signaling receptor binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...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. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsVousden, K.A. / Lundqvist, T. / Popovic, B.
CitationJournal: Sci Rep / Year: 2019
Title: Discovery and characterisation of an antibody that selectively modulates the inhibitory activity of plasminogen activator inhibitor-1.
Authors: Vousden, K.A. / Lundqvist, T. / Popovic, B. / Naiman, B. / Carruthers, A.M. / Newton, P. / Johnson, D.J.D. / Pomowski, A. / Wilkinson, T. / Dufner, P. / de Mendez, I. / Mallinder, P.R. / ...Authors: Vousden, K.A. / Lundqvist, T. / Popovic, B. / Naiman, B. / Carruthers, A.M. / Newton, P. / Johnson, D.J.D. / Pomowski, A. / Wilkinson, T. / Dufner, P. / de Mendez, I. / Mallinder, P.R. / Murray, C. / Strain, M. / Connor, J. / Murray, L.A. / Sleeman, M.A. / Lowe, D.C. / Huntington, J.A. / Vaughan, T.J.
History
DepositionNov 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 13, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Jan 24, 2024Group: 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
Revision 1.4Nov 6, 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: Plasminogen activator inhibitor 1
C: Plasminogen activator inhibitor 1
D: Plasminogen activator inhibitor 1
E: HEAVY CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
F: HEAVY CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
G: HEAVY CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
H: HEAVY CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
I: LIGHT CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
J: LIGHT CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
K: LIGHT CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
L: LIGHT CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY


Theoretical massNumber of molelcules
Total (without water)359,76312
Polymers359,76312
Non-polymers00
Water82946
1
A: Plasminogen activator inhibitor 1
E: HEAVY CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
I: LIGHT CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY


Theoretical massNumber of molelcules
Total (without water)89,9413
Polymers89,9413
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-28 kcal/mol
Surface area33430 Å2
MethodPISA
2
B: Plasminogen activator inhibitor 1
F: HEAVY CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
J: LIGHT CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY


Theoretical massNumber of molelcules
Total (without water)89,9413
Polymers89,9413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-29 kcal/mol
Surface area33730 Å2
MethodPISA
3
C: Plasminogen activator inhibitor 1
G: HEAVY CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
K: LIGHT CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY


Theoretical massNumber of molelcules
Total (without water)89,9413
Polymers89,9413
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-30 kcal/mol
Surface area33900 Å2
MethodPISA
4
D: Plasminogen activator inhibitor 1
H: HEAVY CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY
L: LIGHT CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY


Theoretical massNumber of molelcules
Total (without water)89,9413
Polymers89,9413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-27 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.220, 89.660, 249.770
Angle α, β, γ (deg.)90.00, 99.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Plasminogen activator inhibitor 1 / PAI-1 / Endothelial plasminogen activator inhibitor / Serpin E1


Mass: 42782.023 Da / Num. of mol.: 4 / Mutation: YES [N150H, K154T, Q319L, M354I,]
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1, PAI1, PLANH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05121
#2: Antibody
HEAVY CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY


Mass: 23719.564 Da / Num. of mol.: 4 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody
LIGHT CHAIN OF FAB FRAGMENT FROM AN PAI-1 ANTIBODY


Mass: 23439.076 Da / Num. of mol.: 4 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: ARTIFICIALLY MADE ANTIBODY / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMUTATIONS N150H, K154T, Q319L, M354I

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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: 2.68 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15 MM AMMONIUM ACETATE PH 7.4, 8-10 % PEG 8000, 0.2 M LICL AND 20 % ETHYLENE GLYCOL
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.9→14.99 Å / Num. obs: 86268 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 86.49 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G8R

4g8r


Resolution: 2.9→14.99 Å / Cor.coef. Fo:Fc: 0.8908 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 4316 5 %RANDOM
Rwork0.2192 ---
obs0.2204 86268 99.2 %-
Displacement parametersBiso mean: 63.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.4742 Å20 Å23.3152 Å2
2--0.1297 Å20 Å2
3---0.3445 Å2
Refine analyzeLuzzati coordinate error obs: 0.449 Å
Refinement stepCycle: LAST / Resolution: 2.9→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24572 0 0 46 24618
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125168HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1234176HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8512SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes552HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3648HARMONIC5
X-RAY DIFFRACTIONt_it25168HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion21.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3308SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact26362SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2829 320 5.06 %
Rwork0.2423 5998 -
all0.2445 6318 -
obs--99.2 %
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)
13.1221-0.6398-2.38551.26440.20752.8353-0.1855-0.4286-0.09390.41850.1019-0.01160.19940.20570.0836-0.162-0.031-0.0547-0.13290.0037-0.1419-29.0157-7.4666350.0148
21.0703-0.1428-0.29922.2741.01344.5761-0.0187-0.24320.08690.42630.10190.1404-0.2323-0.097-0.0832-0.1104-0.03540.0748-0.1024-0.0002-0.0914-44.511232.1701358.4575
31.14810.31791.61090.98730.31874.46740.08590.3964-0.0283-0.53390.0674-0.1071-0.11660.321-0.15330.18820.08040.07230.0212-0.0046-0.0775-15.87458.7073274.8405
41.1104-0.0175-0.572.38640.84284.5658-0.11420.4209-0.1818-0.54860.082-0.01780.08640.05030.03220.34540.0606-0.09940.1358-0.0056-0.0153-28.4399-30.9626261.745
51.5003-0.3352-1.73772.47532.01243.6778-0.20370.0211-0.0866-0.42390.2272-0.62140.05440.555-0.0235-0.05520.08560.00590.3040.0150.314910.4643-26.9401303.9083
61.03710.2729-1.38571.7327-1.55447.93220.22980.4934-0.1438-0.5826-0.13260.18820.609-0.4703-0.09720.34530.1117-0.1118-0.0262-0.09470.0578-47.253415.9502296.5801
71.69140.19840.0722.41642.09453.66210.0331-0.2923-0.01020.06250.1596-0.3084-0.10570.5035-0.1927-0.2889-0.12180.09920.1059-0.08330.07315.679927.7298331.7648
80.9569-0.1614-0.77832.5947-1.48876.63760.33420.04960.239-0.2265-0.08250.3314-0.456-0.5408-0.2517-0.15450.02370.0566-0.1909-0.08180.1847-50.7474-15.0565319.4017
90.12-0.2003-0.4332.48581.17840.8336-0.1134-0.0125-0.2555-0.52330.0662-0.17160.14820.18470.04720.02060.12090.02390.0547-0.02540.0302-5.8998-34.4713299.1806
100.6750.0516-0.80621.1977-1.77893.72280.3250.29330.1691-0.4762-0.19450.31030.0334-0.3296-0.13050.22380.1626-0.0498-0.0726-0.0519-0.0036-45.458833.9506295.6625
111.5912-0.0354-0.5462.21711.82612.28090.2305-0.160.6314-0.07590.0545-0.1102-0.4570.1876-0.285-0.1687-0.07760.1195-0.1515-0.05260.0734-11.238535.518330.7568
121.67240.6532-1.81111.3705-1.41254.05090.2356-0.0160.0204-0.1564-0.03040.27170.0503-0.1821-0.2052-0.2365-0.0176-0.039-0.2451-0.0264-0.0597-49.3328-33.0105320.4369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L

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