[English] 日本語
Yorodumi
- PDB-6a8n: The crystal structure of muPAin-1-IG-2 in complex with muPA-SPD a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a8n
TitleThe crystal structure of muPAin-1-IG-2 in complex with muPA-SPD at pH8.5
Components
  • CYS-PRO-ALA-TYR-SER-ARG-TYR-ILE-GLY-CYS
  • Urokinase-type plasminogen activator B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Peptides inhibitor / muPA / serine protease / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Dissolution of Fibrin Clot / regulation of hepatocyte proliferation / skeletal muscle tissue regeneration / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation ...Dissolution of Fibrin Clot / regulation of hepatocyte proliferation / skeletal muscle tissue regeneration / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / serine-type endopeptidase complex / smooth muscle cell migration / plasminogen activation / positive regulation of smooth muscle cell migration / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / Neutrophil degranulation / positive regulation of reactive oxygen species metabolic process / peptidase activity / regulation of cell population proliferation / angiogenesis / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / positive regulation of cell population proliferation / extracellular space
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. / EGF-like domain signature 1. ...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, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesMus musculus (house mouse)
Phage display vector pTDisp (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.489 Å
AuthorsWang, D. / Yang, Y.S. / Jiang, L.G. / Huang, M.D. / Li, J.Y. / Andreasen, P.A. / Xu, P. / Chen, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China21708043 China
National Natural Science Foundation of China81572944 China
National Natural Science Foundation of ChinaU1405229 China
CitationJournal: J.Med.Chem. / Year: 2019
Title: Suppression of Tumor Growth and Metastases by Targeted Intervention in Urokinase Activity with Cyclic Peptides.
Authors: Wang, D. / Yang, Y. / Jiang, L. / Wang, Y. / Li, J. / Andreasen, P.A. / Chen, Z. / Huang, M. / Xu, P.
History
DepositionJul 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Urokinase-type plasminogen activator B
P: CYS-PRO-ALA-TYR-SER-ARG-TYR-ILE-GLY-CYS
B: Urokinase-type plasminogen activator B
C: CYS-PRO-ALA-TYR-SER-ARG-TYR-ILE-GLY-CYS


Theoretical massNumber of molelcules
Total (without water)57,3754
Polymers57,3754
Non-polymers00
Water00
1
A: Urokinase-type plasminogen activator B
P: CYS-PRO-ALA-TYR-SER-ARG-TYR-ILE-GLY-CYS


Theoretical massNumber of molelcules
Total (without water)28,6872
Polymers28,6872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-8 kcal/mol
Surface area11130 Å2
MethodPISA
2
B: Urokinase-type plasminogen activator B
C: CYS-PRO-ALA-TYR-SER-ARG-TYR-ILE-GLY-CYS


Theoretical massNumber of molelcules
Total (without water)28,6872
Polymers28,6872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.028, 112.028, 102.214
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

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


Mass: 27554.158 Da / Num. of mol.: 2 / Mutation: C301A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plau
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P06869, u-plasminogen activator
#2: Protein/peptide CYS-PRO-ALA-TYR-SER-ARG-TYR-ILE-GLY-CYS / muPAin-1-IG-2


Mass: 1133.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Phage display vector pTDisp (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 80 mM Tris-HCl pH 8.5, 1.6 M NaH2PO4, 20% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26314 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 38.16 Å2 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.046 / Rrim(I) all: 0.195 / Χ2: 2.321 / Net I/σ(I): 5.3 / Num. measured all: 490887
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.54200.44112720.9720.10.4530.981100
2.54-2.5919.70.39812850.9760.0920.4081.076100
2.59-2.6419.50.38412950.9780.0890.3941.09100
2.64-2.6919.30.37813150.9740.0880.3881.112100
2.69-2.7518.70.3413060.9750.0820.351.311100
2.75-2.8217.70.32813040.9740.0810.3381.362100
2.82-2.89190.32112990.9710.0760.331.5100
2.89-2.9620.30.29112910.9840.0660.2991.734100
2.96-3.05200.27413110.9840.0630.2811.939100
3.05-3.1519.70.25512980.9850.0590.2622.243100
3.15-3.2619.70.23612940.9890.0550.2432.382100
3.26-3.3919.30.22213350.9890.0530.2282.656100
3.39-3.5518.30.20113060.9910.050.2072.995100
3.55-3.7316.70.18113050.9910.0470.1873.244100
3.73-3.9718.90.17713230.9920.0430.1833.446100
3.97-4.2718.40.16113200.9930.0390.1663.796100
4.27-4.717.90.1513360.9940.0370.1553.893100
4.7-5.3816.60.1513380.9940.0390.1553.658100
5.38-6.7818.10.15513470.9930.0380.163.381100
6.78-5015.60.12814340.9940.0340.1333.1799.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.94 Å35.18 Å
Translation3.94 Å35.18 Å

-
Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A8G

6a8g


Resolution: 2.489→35.184 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 1322 5.04 %
Rwork0.2036 24907 -
obs0.2062 26229 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.33 Å2 / Biso mean: 43.1387 Å2 / Biso min: 18.22 Å2
Refinement stepCycle: final / Resolution: 2.489→35.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4006 0 0 0 4006
Num. residues----510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4893-2.58890.29831290.23462660278998
2.5889-2.70670.29831550.219227422897100
2.7067-2.84940.28011590.217827412900100
2.8494-3.02780.32841550.218327452900100
3.0278-3.26140.25871510.203127352886100
3.2614-3.58940.27641540.201527812935100
3.5894-4.10810.2081360.180327842920100
4.1081-5.17310.21411190.182228442963100
5.1731-35.18740.25331640.2272875303998
Refinement TLS params.Method: refined / Origin x: -33.4873 Å / Origin y: 32.9498 Å / Origin z: -47.111 Å
111213212223313233
T0.2168 Å2-0.0265 Å2-0.0347 Å2-0.2732 Å2-0.0427 Å2--0.2672 Å2
L0.8061 °20.0839 °2-0.5916 °2-0.5457 °20.1872 °2--1.3781 °2
S0.0256 Å °-0.0052 Å °0.0027 Å °-0.0332 Å °0.0979 Å °-0.1308 Å °-0.0094 Å °0.2171 Å °-0.1092 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 243
2X-RAY DIFFRACTION1allP1 - 10
3X-RAY DIFFRACTION1allB16 - 243
4X-RAY DIFFRACTION1allC1 - 10

+
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://pdbjlvh1.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