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- PDB-5zlz: Structure of tPA and PAI-1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5zlz
TitleStructure of tPA and PAI-1
Components
  • Plasminogen activator inhibitor 1
  • Tissue-type plasminogen activator
KeywordsHYDROLASE INHIBITOR/HYDROLASE / PAI-1 / fibrinolysis / PAItrap2 / HYDROLASE INHIBITOR-HYDROLASE complex
Function / homology
Function and homology information


t-plasminogen activator / positive regulation of leukotriene production involved in inflammatory response / negative regulation of smooth muscle cell-matrix adhesion / prevention of polyspermy / negative regulation of integrin-mediated signaling pathway / trans-synaptic signaling by BDNF, modulating synaptic transmission / dentinogenesis / positive regulation of coagulation / negative regulation of vascular wound healing / negative regulation of smooth muscle cell migration ...t-plasminogen activator / positive regulation of leukotriene production involved in inflammatory response / negative regulation of smooth muscle cell-matrix adhesion / prevention of polyspermy / negative regulation of integrin-mediated signaling pathway / trans-synaptic signaling by BDNF, modulating synaptic transmission / dentinogenesis / positive regulation of coagulation / negative regulation of vascular wound healing / 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 wound healing / positive regulation of odontoblast differentiation / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / negative regulation of cell adhesion mediated by integrin / positive regulation of monocyte chemotaxis / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / endopeptidase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / replicative senescence / negative regulation of blood coagulation / negative regulation of fibrinolysis / positive regulation of blood coagulation / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ECM proteoglycans / fibrinolysis / negative regulation of proteolysis / BMAL1:CLOCK,NPAS2 activates circadian expression / secretory granule / platelet alpha granule lumen / negative regulation of cell migration / protein modification process / positive regulation of interleukin-8 production / serine-type endopeptidase inhibitor activity / phosphoprotein binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of receptor-mediated endocytosis / Schaffer collateral - CA1 synapse / positive regulation of angiogenesis / blood coagulation / positive regulation of inflammatory response / apical part of cell / Platelet degranulation / cellular response to lipopolysaccharide / angiogenesis / protease binding / extracellular matrix / defense response to Gram-negative bacterium / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / cell surface / proteolysis / : / extracellular exosome / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Tissue plasminogen activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 ...Tissue plasminogen activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / 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 / EGF-like domain / 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 signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tissue-type plasminogen activator / Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.581 Å
AuthorsMin, L. / Huang, M.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370737 China
National Natural Science Foundation of China31400637 China
National Natural Science Foundation of China31570745 China
National Natural Science Foundation of China31670739 China
National Natural Science Foundation of ChinaU1405229 China
CitationJournal: To Be Published
Title: Development of a PAI-1 trapping agent (PAItrap2) based on inactivated tPA-SPD and the crystal structure of PAItrap2 in complex with PAI-1
Authors: Min, L. / Huang, M.
History
DepositionMar 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Plasminogen activator inhibitor 1
E: Tissue-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4054
Polymers70,2212
Non-polymers1842
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-1 kcal/mol
Surface area26050 Å2
Unit cell
Length a, b, c (Å)49.852, 67.186, 212.591
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 / PAI-1 / Endothelial plasminogen activator inhibitor / Serpin E1


Mass: 42212.379 Da / Num. of mol.: 1 / Mutation: N173H, K177T, Q342L, M377I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1, PAI1, PLANH1
Production host: prokaryotic environmental samples (environmental samples)
References: UniProt: P05121
#2: Protein Tissue-type plasminogen activator / tPA


Mass: 28008.666 Da / Num. of mol.: 1 / Mutation: C430A, F458E, N483Q, S513A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAT
Production host: prokaryotic environmental samples (environmental samples)
References: UniProt: P00750, t-plasminogen activator
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4-8% PEG 3350, 20 mM bis-Tris-HCl pH 7.0

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.581→48.535 Å / Num. obs: 8956 / % possible obs: 99.97 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 7.6
Reflection shellResolution: 3.581→3.709 Å / Rmerge(I) obs: 0.561

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A5H, 3PB1

1a5h

3pb1


Resolution: 3.581→48.535 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.81
RfactorNum. reflection% reflection
Rfree0.3122 406 5.33 %
Rwork0.2226 --
obs0.2275 7618 85.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.581→48.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4879 0 12 0 4891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035012
X-RAY DIFFRACTIONf_angle_d0.5886801
X-RAY DIFFRACTIONf_dihedral_angle_d5.4632988
X-RAY DIFFRACTIONf_chiral_restr0.042760
X-RAY DIFFRACTIONf_plane_restr0.005874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.581-4.09890.32191100.21981802X-RAY DIFFRACTION66
4.0989-5.16320.28891500.22632563X-RAY DIFFRACTION92
5.1632-48.53980.33011460.22112847X-RAY DIFFRACTION97
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)
10.1319-0.14-0.3321.4868-0.46031.1377-0.26570.2276-0.24090.1271-0.3897-0.20390.22710.0303-0.2865-0.0171-0.21780.1548-0.3064-0.10730.57858.306-11.9092-62.5545
23.81580.16680.06421.1568-0.03230.24020.11550.91820.1278-0.1567-0.00640.02190.03020.0888-0.0001-0.0909-0.02060.15260.1744-0.10710.56967.4174-5.523-66.5897
32.5440.430.3631.41680.27550.8901-0.09040.61970.0524-0.42880.0302-0.3156-0.02760.1740.06610.1958-0.05040.40580.27750.32350.44526.56870.7637-66.6316
41.73720.2406-0.040.2305-0.15520.0930.03110.13650.2434-0.4432-0.1051-0.22570.11970.18780.1056-0.09410.57950.6378-0.0347-0.21740.644513.6548-9.0601-66.6227
50.1335-0.33970.04191.69530.12870.2952-0.08240.04810.0533-0.2827-0.097-0.28390.1157-0.0059-0.14930.24840.00680.7920.2272-0.19141.015410.39426.67-68.1929
62.0515-0.39050.07030.15950.25140.7910.2016-0.05640.68820.198-0.02890.059-0.24830.2033-0.31620.15230.00260.29810.2212-0.16330.65792.55817.1251-60.7969
71.3351-0.09661.94294.83051.89853.6913-0.51810.7519-0.2231-1.04880.5986-0.8722-0.20580.5176-0.30150.68410.23840.21510.8265-0.31130.463511.6281-7.5096-80.4433
84.2297-0.2803-2.97942.53540.12172.1009-0.09680.841-0.1986-0.20520.20520.10680.2336-0.45220.14550.41860.11870.05890.7915-0.28690.3022-1.4448-6.5874-76.9056
96.50444.5462-7.42073.7967-4.1011.99990.2251.59441.6276-0.12820.23450.7193-0.6902-1.3719-0.4260.72770.2235-0.29061.0704-0.03770.7418-14.91072.1081-72.9495
100.27320.28190.17740.35040.39510.9455-0.1710.1280.1149-0.1076-0.24510.5217-0.1499-0.3502-0.1389-0.02930.1914-0.2625-0.07830.05380.8193-6.4473-11.2117-58.9361
110.25870.0683-0.03650.0965-0.00130.211-0.00360.0115-0.12550.0084-0.00190.01760.0609-0.00190.1318-0.1602-0.09770.3417-0.0552-0.01170.32516.3347-17.1958-56.4653
120.471-0.2553-0.0850.66-0.17990.11650.15260.0076-0.0262-0.08880.10130.16870.0417-0.1174-0.02010.2273-0.01410.0629-0.1305-0.08340.8729-12.6704-8.5488-60.3995
130.5680.50590.06760.4659-0.05050.7528-0.0349-0.07770.06610.0194-0.19080.17490.0084-0.35110.05870.24620.23830.40710.6323-0.14680.5811-16.41563.1582-51.4411
141.03040.390.26091.36460.09630.3157-0.1772-0.414-0.21260.46350.1391-0.02310.1489-0.1182-0.0285-0.06290.26120.1333-0.46970.08010.5924-11.5171-3.4462-53.7749
150.3629-0.34070.00060.37640.00010.20180.03730.0107-0.1619-0.1686-0.00990.20490.0007-0.1091-0.08420.08530.0639-0.0575-0.05310.19480.6135-3.4935-10.6286-54.7524
166.87581.5954-0.96.67091.00013.7332-0.13091.08150.1155-0.56270.00210.7945-0.2546-0.54080.0641-0.02460.26080.00060.3291-0.06340.2726-5.2679-7.1385-66.6932
171.0911-0.4816-0.59255.5197-1.4560.87560.20810.7755-0.228-0.76270.06970.99510.13480.0711-0.26940.56050.4045-0.11971.05970.10490.4928-9.5779-6.3714-74.6172
181.8038-0.5976-0.46560.8053-0.72741.92230.2350.17850.0292-0.04250.13910.0714-0.0951-0.1846-0.1341-0.2780.20570.14710.221-0.3450.3947-6.08420.0594-60.3996
190.0288-0.2773-0.03192.67630.79472.319-0.12850.990.82-1.1244-0.1275-0.1394-0.25190.41480.23790.99950.2410.04760.89420.50460.64344.95599.3098-78.3122
201.36230.70650.13611.5175-0.3831.47040.20690.3028-0.20710.30440.3805-0.1338-0.26890.3363-0.33211.2363-0.2497-0.21830.824-0.03940.350126.48914.6426-22.0304
210.67180.4961-1.64825.86040.07536.21430.2141-0.81250.46970.78110.41230.0039-0.7147-0.1007-0.62451.9563-0.17460.11731.1264-0.03350.717432.799214.9186-8.7398
221.8035-0.1215-0.49373.83880.70193.02270.0428-0.33810.61480.28710.4562-0.0407-0.9339-0.3445-0.5281.63590.13630.09130.79730.18680.840921.743319.6155-16.822
231.2426-0.26940.27160.5342-0.30311.3830.1932-0.46050.13620.55280.35050.0689-0.2216-0.0159-0.28371.8711-0.21840.18511.65360.13030.328516.186611.3219-6.133
243.79081.41052.65822.3285-0.01592.5668-0.2398-1.25960.46690.7433-0.15460.1664-0.5767-0.60080.4442.72940.64640.00982.1938-0.26260.910419.64420.8018-4.6423
250.4248-0.0412-0.15370.00350.02160.05310.1256-1.1135-0.23071.11270.058-0.24780.2793-0.3292-0.07322.4195-0.1574-0.00392.00540.17640.348815.56530.3753-3.8228
263.41470.95261.63352.35270.84214.48660.3415-0.6235-0.0760.9331-0.19170.40090.2654-0.6878-0.11150.7580.01670.20010.41750.06310.92964.6691-5.7492-36.2973
272.22110.5746-1.63880.5585-0.31131.24070.1178-0.4783-0.87711.54970.0461-0.54180.82730.3204-0.16861.57950.015-0.29550.57140.2871.766422.1576-17.3712-34.2824
281.3062-1.4840.02222.45820.58540.48520.2057-0.1757-0.23040.6013-0.1539-0.02420.18670.0683-0.07360.8545-0.363-0.05710.26830.05471.001612.067-14.6514-34.9856
295.99952.1422-1.67473.31590.3744.1320.102-0.0692-0.26770.37460.0932-0.5018-0.54580.2802-0.18040.40320.0453-0.17250.1205-0.13960.390415.19922.3121-44.5734
300.11480.6186-0.23223.3434-1.25550.47140.03210.234-0.38150.0518-0.0327-0.0805-0.12880.3219-0.06260.4031-0.20830.00551.2390.08641.145434.6193-0.3389-41.7546
313.4641-2.8875-2.90753.83872.05753.0966-0.0763-0.39770.00590.2192-0.0031-0.2529-0.01030.83630.09350.1732-0.1164-0.14840.7734-0.10680.926124.4546-0.6174-42.3811
324.7981-0.65770.34514.38022.89724.64350.0451-0.61640.21940.6168-0.11730.4729-0.7834-0.65170.12890.44250.21320.29160.3211-0.01080.397713.31675.1475-34.2674
335.93562.02732.42116.16920.26937.403-0.0062-0.3522-0.95580.79390.2716-0.42270.4511.2498-0.24830.52220.13210.08141.04460.03450.495930.0364-5.2928-36.476
343.59940.72051.23310.85250.37354.4212-0.1538-0.23550.42240.76330.2568-0.1188-1.00840.2631-0.06130.5304-0.0137-0.31960.17130.0380.707718.94074.9934-41.0633
350.5675-0.10380.39072.5793-0.60554.40040.4281-0.79940.5491.17030.07230.0635-0.2982-0.2269-0.41361.76320.0456-0.05811.0837-0.24620.702130.59173.7349-8.4583
361.4733-1.058-0.47491.7016-0.40264.57310.0001-0.36670.27290.6370.35720.1266-0.3913-1.2428-0.21511.2632-0.21230.02051.06380.18020.341918.2915-0.4814-14.5103
377.9117-0.184.47463.46272.41044.35530.25840.18610.4429-0.4944-0.05740.9712-0.5522-3.5426-0.19081.50150.02720.07122.97230.22851.0302-4.6922-2.0353-33.829
380.81910.68130.70531.21960.4160.6369-0.1593-0.11190.2025-0.0033-0.09030.2588-0.2355-0.22250.17310.565-0.01540.0039-0.0526-0.16760.05287.9398-5.3176-47.7068
393.67441.53441.36514.441.19393.88060.16390.0283-0.62040.74850.3611-0.4964-0.0718-0.5266-0.38750.87720.0846-0.21210.3949-0.04320.341319.44021.3609-29.4181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain E and resid 16:38)
2X-RAY DIFFRACTION2(chain E and resid 39:49)
3X-RAY DIFFRACTION3(chain E and resid 50:59)
4X-RAY DIFFRACTION4(chain E and resid 60:84)
5X-RAY DIFFRACTION5(chain E and resid 85:92)
6X-RAY DIFFRACTION6(chain E and resid 93:107)
7X-RAY DIFFRACTION7(chain E and resid 108:117)
8X-RAY DIFFRACTION8(chain E and resid 118:124)
9X-RAY DIFFRACTION9(chain E and resid 125:130)
10X-RAY DIFFRACTION10(chain E and resid 131:148)
11X-RAY DIFFRACTION11(chain E and resid 149:155)
12X-RAY DIFFRACTION12(chain E and resid 156:166)
13X-RAY DIFFRACTION13(chain E and resid 167:170)
14X-RAY DIFFRACTION14(chain E and resid 171:187)
15X-RAY DIFFRACTION15(chain E and resid 188:192)
16X-RAY DIFFRACTION16(chain E and resid 193:203)
17X-RAY DIFFRACTION17(chain E and resid 204:211)
18X-RAY DIFFRACTION18(chain E and resid 212:238)
19X-RAY DIFFRACTION19(chain E and resid 239:243)
20X-RAY DIFFRACTION20(chain I and resid 6:43)
21X-RAY DIFFRACTION21(chain I and resid 44:59)
22X-RAY DIFFRACTION22(chain I and resid 60:83)
23X-RAY DIFFRACTION23(chain I and resid 86:108)
24X-RAY DIFFRACTION24(chain I and resid 109:120)
25X-RAY DIFFRACTION25(chain I and resid 121:172)
26X-RAY DIFFRACTION26(chain I and resid 173:187)
27X-RAY DIFFRACTION27(chain I and resid 188:195)
28X-RAY DIFFRACTION28(chain I and resid 196:203)
29X-RAY DIFFRACTION29(chain I and resid 204:213)
30X-RAY DIFFRACTION30(chain I and resid 214:219)
31X-RAY DIFFRACTION31(chain I and resid 220:224)
32X-RAY DIFFRACTION32(chain I and resid 225:240)
33X-RAY DIFFRACTION33(chain I and resid 241:254)
34X-RAY DIFFRACTION34(chain I and resid 255:276)
35X-RAY DIFFRACTION35(chain I and resid 277:313)
36X-RAY DIFFRACTION36(chain I and resid 314:332)
37X-RAY DIFFRACTION37(chain I and resid 333:339)
38X-RAY DIFFRACTION38(chain I and resid 340:355)
39X-RAY DIFFRACTION39(chain I and resid 356:379)

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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