[English] 日本語
Yorodumi
- PDB-6gwn: Crystal Structure of Stabilized Active Plasminogen Activator Inhi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gwn
TitleCrystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F) in Complex with Two Inhibitory Nanobodies (VHH-2g-42, VHH-2w-64)
Components
  • Plasminogen activator inhibitor 1
  • VHH-2g-42
  • VHH-2w-64
KeywordsHYDROLASE / plasminogen activator inhibitor-1 / PAI-1 / PAI-1-W175F / serpin / protease inhibitor / serine protease inhibitor / nanobody / antibody fragment / protein complex
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 / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of smooth muscle cell migration / 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 / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of smooth muscle cell migration / 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 / positive regulation of monocyte chemotaxis / Dissolution of Fibrin Clot / 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 / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of interleukin-8 production / serine-type endopeptidase inhibitor activity / positive regulation of receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsSillen, M. / Weeks, S.D. / Strelkov, S.V. / Declerck, P.J.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - FlandersG072915N Belgium
Research Foundation - Flanders11ZQ916N Belgium
CitationJournal: J.Thromb.Haemost. / Year: 2020
Title: Molecular mechanism of two nanobodies that inhibit PAI-1 activity reveals a modulation at distinct stages of the PAI-1/plasminogen activator interaction.
Authors: Sillen, M. / Weeks, S.D. / Zhou, X. / Komissarov, A.A. / Florova, G. / Idell, S. / Strelkov, S.V. / Declerck, P.J.
History
DepositionJun 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plasminogen activator inhibitor 1
B: VHH-2g-42
C: VHH-2w-64


Theoretical massNumber of molelcules
Total (without water)68,6203
Polymers68,6203
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-12 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.483, 71.424, 96.598
Angle α, β, γ (deg.)90.000, 100.530, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 42780.031 Da / Num. of mol.: 1 / Mutation: W175F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1, PAI1, PLANH1 / Plasmid: pETHSUK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS / References: UniProt: P05121
#2: Antibody VHH-2g-42


Mass: 12752.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pETHSUK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS
#3: Antibody VHH-2w-64


Mass: 13087.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pETHSUK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris, 10 % w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2017
Details: CRL combinations for vertical focussing and an eliptical mirror for horizontal focussing
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.96→94.97 Å / Num. obs: 42665 / % possible obs: 98.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 38.93 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.96-2.073.60.78361000.7570.4790.92196.5
6.21-94.973.30.04314090.9950.0270.05197.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSJun 1, 2017 BUILT=20170923data reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q02, 5JA8, 5JA9

3q02

5ja8

5ja9


Resolution: 2.03→94.97 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 32.84
RfactorNum. reflection% reflection
Rfree0.2499 1956 5.06 %
Rwork0.2083 --
obs0.2103 38685 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.9 Å2 / Biso mean: 55.7968 Å2 / Biso min: 27.91 Å2
Refinement stepCycle: final / Resolution: 2.03→94.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4567 0 0 109 4676
Biso mean---51.87 -
Num. residues----595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074671
X-RAY DIFFRACTIONf_angle_d1.066346
X-RAY DIFFRACTIONf_chiral_restr0.075714
X-RAY DIFFRACTIONf_plane_restr0.006819
X-RAY DIFFRACTIONf_dihedral_angle_d13.3991659
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.08080.41081360.36342509264594
2.0808-2.13710.36881460.32822578272498
2.1371-2.19990.34021380.30832599273798
2.1999-2.2710.31951550.29592608276398
2.271-2.35210.32671590.28122600275998
2.3521-2.44630.35951420.27152586272898
2.4463-2.55770.36581380.26092640277898
2.5577-2.69250.32861150.2482629274498
2.6925-2.86120.33421230.23812671279499
2.8612-3.08210.2761400.23782628276899
3.0821-3.39230.26311400.22332661280199
3.3923-3.88320.23871340.19552639277398
3.8832-4.89240.17841340.15122682281699
4.8924-95.07370.18051560.15862699285598
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)
11.4521-0.96491.2531.5151-1.44212.261-0.04780.24130.18270.03270.0309-0.0341-0.17380.00380.02040.2818-0.0260.01860.43060.0790.3626-27.9566-8.4636-21.097
24.573-0.1468-1.67772.28631.11964.03740.04580.28830.1667-0.29990.0879-0.16360.0630.379-0.08160.40630.05260.00210.8080.19820.3846-13.0192-4.7951-55.5578
32.68610.0784-0.52915.1878-0.35463.7918-0.08870.3904-0.129-0.1681-0.0051-0.31070.37440.02250.07330.2684-0.00280.02410.4395-0.01320.2632-7.1446-41.0296-10.1184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 379 )A1 - 379
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 115 )B1 - 115
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 120 )C2 - 120

+
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