[English] 日本語
Yorodumi
- PDB-8uct: Crystal structure of TcPINK1 in complex with PRT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uct
TitleCrystal structure of TcPINK1 in complex with PRT
ComponentsSerine/threonine-protein kinase Pink1, mitochondrial
KeywordsCELL CYCLE / Mitophagy Autophagy Kinase
Function / homology
Function and homology information


positive regulation of free ubiquitin chain polymerization / autophagy of mitochondrion / positive regulation of mitochondrial fission / positive regulation of protein ubiquitination / protein autophosphorylation / regulation of apoptotic process / mitochondrial outer membrane / non-specific serine/threonine protein kinase / mitochondrial inner membrane / protein serine/threonine kinase activity ...positive regulation of free ubiquitin chain polymerization / autophagy of mitochondrion / positive regulation of mitochondrial fission / positive regulation of protein ubiquitination / protein autophosphorylation / regulation of apoptotic process / mitochondrial outer membrane / non-specific serine/threonine protein kinase / mitochondrial inner membrane / protein serine/threonine kinase activity / ubiquitin protein ligase binding / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-3YT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Serine/threonine-protein kinase Pink1, mitochondrial
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsVeyron, S. / Rasool, S. / Trempe, J.F.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)153274 Canada
Michael J. Fox Foundation12119 United States
CitationJournal: Sci Rep / Year: 2024
Title: Identification and structural characterization of small molecule inhibitors of PINK1.
Authors: Rasool, S. / Shomali, T. / Truong, L. / Croteau, N. / Veyron, S. / Bustillos, B.A. / Springer, W. / Fiesel, F.C. / Trempe, J.F.
History
DepositionSep 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase Pink1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7725
Polymers51,0321
Non-polymers7404
Water41423
1
A: Serine/threonine-protein kinase Pink1, mitochondrial
hetero molecules

A: Serine/threonine-protein kinase Pink1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,54410
Polymers102,0652
Non-polymers1,4808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5140 Å2
ΔGint-91 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.216, 53.216, 545.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein Serine/threonine-protein kinase Pink1, mitochondrial


Mass: 51032.293 Da / Num. of mol.: 1 / Mutation: W131A, W142A, Y225A, Y378A, F401A, F437A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: Pink1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D6WMX4
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-3YT / 2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-{[3-(2H-1,2,3-triazol-2-yl)phenyl]amino}pyrimidine-5-carboxamide


Mass: 393.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N9O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM HEPES, PEG 4000, 150mM ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.93→90.93 Å / Num. obs: 11014 / % possible obs: 100 % / Redundancy: 17.8 % / Biso Wilson estimate: 75.42 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.145 / Net I/σ(I): 6.1
Reflection shellResolution: 2.93→2.98 Å / Redundancy: 16.9 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 521 / CC1/2: 0.551 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→90.93 Å / SU ML: 0.4527 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3052 546 5.04 %
Rwork0.2834 10293 -
obs0.2845 10839 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.82 Å2
Refinement stepCycle: LAST / Resolution: 2.93→90.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 47 23 3051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663092
X-RAY DIFFRACTIONf_angle_d0.77614217
X-RAY DIFFRACTIONf_chiral_restr0.0423489
X-RAY DIFFRACTIONf_plane_restr0.0126547
X-RAY DIFFRACTIONf_dihedral_angle_d16.61971123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.230.37251150.39192308X-RAY DIFFRACTION93.48
3.23-3.70.39021430.33832535X-RAY DIFFRACTION99.93
3.7-4.660.2831240.25592612X-RAY DIFFRACTION99.93
4.66-90.930.2781640.25772838X-RAY DIFFRACTION99.97

+
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