[English] 日本語
Yorodumi
- PDB-7zrr: Crystal structure of human Urokinase-type plasminogen activator i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zrr
TitleCrystal structure of human Urokinase-type plasminogen activator in complex with bicycle peptide inhibitor UK965
Components
  • Urokinase-type plasminogen activator
  • synthetic peptide UK965
KeywordsHYDROLASE / Urokinase-type plasminogen activator / Serine protease / Plasminogen Activator
Function / homology
Function and homology information


u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. ...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 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
AMINO GROUP / 1,3,5-tris(bromomethyl)benzene / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsCaregnato, A. / Angela, P. / Mazzoccato, Y. / Frasson, N. / Angelini, A. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: To Be Published
Title: Crystal structure of human Urokinase-type plasminogen activator in complex with bicycle peptide inhibitor UK965
Authors: Caregnato, A. / Angela, P. / Mazzoccato, Y. / Frasson, N. / Angelini, A. / Cendron, L.
History
DepositionMay 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Urokinase-type plasminogen activator
B: synthetic peptide UK965
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3267
Polymers33,5902
Non-polymers7355
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.906, 120.906, 42.716
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Urokinase-type plasminogen activator / U-plasminogen activator / uPA


Mass: 31872.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Cell line (production host): human embryonic kidney cells / Production host: Homo sapiens (human) / References: UniProt: P00749, u-plasminogen activator
#2: Protein/peptide synthetic peptide UK965


Mass: 1717.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): human embryonic kidney cells / Production host: Homo sapiens (human)

-
Non-polymers , 5 types, 130 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZBR / 1,3,5-tris(bromomethyl)benzene


Mass: 356.880 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H9Br3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: 5% PEG400, 50mM Citrato pH 4.3, 1.8 M (NH4)2SO4, 20% Ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.64→39.58 Å / Num. obs: 28238 / % possible obs: 99.3 % / Redundancy: 7.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Net I/σ(I): 8.5
Reflection shellResolution: 1.64→1.8 Å / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1430 / CC1/2: 0.317

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qn7

3qn7


Resolution: 1.64→33.12 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.054 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 1353 4.9 %RANDOM
Rwork0.2012 ---
obs0.2031 26428 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.67 Å2 / Biso mean: 24.776 Å2 / Biso min: 9.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.64→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 34 125 2226
Biso mean--45.19 30.08 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122240
X-RAY DIFFRACTIONr_angle_refined_deg1.551.6463029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9015278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.14120.776116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5851518
X-RAY DIFFRACTIONr_chiral_restr0.110.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021702
LS refinement shellResolution: 1.643→1.686 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 83 -
Rwork0.323 1929 -
all-2012 -
obs--96.5 %

+
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://pdbjlc1.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