[English] 日本語
Yorodumi
- PDB-5brr: Michaelis complex of tPA-S195A:PAI-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5brr
TitleMichaelis complex of tPA-S195A:PAI-1
Components
  • Plasminogen activator inhibitor 1
  • Tissue-type plasminogen activator
KeywordsHYDROLASE INHIBITOR/HYDROLASE / Tissue-Type Plasminogen Activator Catalytic Domain / Plasminogen Activator Inhibitor 1 / Structure-Activity Relationship / Thrombolysis / HYDROLASE INHIBITOR-HYDROLASE complex
Function / homology
Function and homology information


t-plasminogen activator / trans-synaptic signaling by BDNF, modulating synaptic transmission / positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / prevention of polyspermy / negative regulation of smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of coagulation / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of vascular wound healing ...t-plasminogen activator / trans-synaptic signaling by BDNF, modulating synaptic transmission / positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / prevention of polyspermy / negative regulation of smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of coagulation / 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 smooth muscle cell migration / negative regulation of endopeptidase activity / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / Signaling by PDGF / negative regulation of plasminogen activation / regulation of signaling receptor activity / positive regulation of monocyte chemotaxis / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / 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 / negative regulation of cell migration / platelet alpha granule lumen / secretory granule / positive regulation of interleukin-8 production / phosphoprotein binding / serine-type endopeptidase inhibitor activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / protein modification process / Schaffer collateral - CA1 synapse / positive regulation of receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / blood coagulation / apical part of cell / Platelet degranulation / cellular response to lipopolysaccharide / protease binding / : / defense response to Gram-negative bacterium / angiogenesis / response to hypoxia / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / cell surface / proteolysis / extracellular space / 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. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / 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
TRIETHYLENE GLYCOL / Tissue-type plasminogen activator / Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.16 Å
AuthorsGong, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31170707 China
National Natural Science Foundation of China31370737 China
CAS/SFEA International Partnership Program for Creative Research Teams China
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of the Michaelis Complex between Tissue-type Plasminogen Activator and Plasminogen Activators Inhibitor-1
Authors: Gong, L. / Liu, M. / Zeng, T. / Shi, X. / Yuan, C. / Andreasen, P.A. / Huang, M.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Nov 11, 2015Group: Database references
Revision 1.4Oct 18, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,4247
Polymers70,9062
Non-polymers5195
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-4 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.740, 73.940, 201.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 42782.023 Da / Num. of mol.: 1 / Mutation: 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: Protein Tissue-type plasminogen activator / tPA


Mass: 28123.844 Da / Num. of mol.: 1 / Fragment: UNP residues 311-562 / Mutation: C120A, N173Q, S203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAT / Production host: Komagataella pastoris CBS 7435 (fungus) / Strain (production host): X-33 / References: UniProt: P00750, t-plasminogen activator
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 8% PEG 6000, 0.1 M Tris-HCl

-
Data collection

DiffractionMean temperature: 100 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: 3.16→35.43 Å / Num. obs: 13390 / % possible obs: 99.9 % / Redundancy: 6.9 % / Net I/σ(I): 6.9
Reflection shellHighest resolution: 3.16 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOLREPmodel building
HKL-2000data collection
RefinementResolution: 3.16→35.43 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.852 / SU B: 25.619 / SU ML: 0.448 / Cross valid method: FREE R-VALUE / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27596 662 4.9 %RANDOM
Rwork0.20349 ---
obs0.2071 12728 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.843 Å2
Baniso -1Baniso -2Baniso -3
1--3.55 Å20 Å2-0 Å2
2---2.61 Å20 Å2
3---6.16 Å2
Refinement stepCycle: 1 / Resolution: 3.16→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 34 36 4988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195045
X-RAY DIFFRACTIONr_bond_other_d0.0090.024818
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9556791
X-RAY DIFFRACTIONr_angle_other_deg0.885311061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6885596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47923.636231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.61115849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2291534
X-RAY DIFFRACTIONr_chiral_restr0.0730.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215515
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021167
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_it2.4374.6632465
X-RAY DIFFRACTIONr_mcbond_other2.4354.6622464
X-RAY DIFFRACTIONr_mcangle_it4.1186.9723034
X-RAY DIFFRACTIONr_mcangle_other4.1186.9733035
X-RAY DIFFRACTIONr_scbond_it2.1944.9322580
X-RAY DIFFRACTIONr_scbond_other2.1934.9322580
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.737.2913758
X-RAY DIFFRACTIONr_long_range_B_refined7.13537.7275905
X-RAY DIFFRACTIONr_long_range_B_other7.13537.7295906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.16→3.242 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 59 -
Rwork0.238 893 -
obs--99.79 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more