[English] 日本語
Yorodumi
- PDB-6hue: ParkinS65N -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hue
TitleParkinS65N
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / E3 ligase
Function / homology
Function and homology information


positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / cellular response to L-glutamine / : / negative regulation of exosomal secretion ...positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / cellular response to L-glutamine / : / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / aggresome assembly / negative regulation of glucokinase activity / response to curcumin / protein K29-linked ubiquitination / free ubiquitin chain polymerization / cellular response to hydrogen sulfide / negative regulation of mitochondrial fusion / positive regulation of protein linear polyubiquitination / RBR-type E3 ubiquitin transferase / regulation of dopamine metabolic process / Parkin-FBXW7-Cul1 ubiquitin ligase complex / positive regulation of mitochondrial fusion / negative regulation of actin filament bundle assembly / regulation of synaptic vesicle transport / mitochondrial fragmentation involved in apoptotic process / host-mediated suppression of viral genome replication / positive regulation of mitophagy / F-box domain binding / regulation of necroptotic process / regulation of cellular response to oxidative stress / positive regulation of dendrite extension / positive regulation of type 2 mitophagy / negative regulation of excitatory postsynaptic potential / cellular response to L-glutamate / autophagy of mitochondrion / dopaminergic synapse / aggresome / mitochondrial fission / mitochondrion localization / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein localization to mitochondrion / cellular response to dopamine / cellular response to toxic substance / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of protein localization to membrane / regulation of mitochondrion organization / protein K11-linked ubiquitination / negative regulation of reactive oxygen species metabolic process / protein K6-linked ubiquitination / neuron cellular homeostasis / positive regulation of proteasomal protein catabolic process / negative regulation of JNK cascade / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / positive regulation of mitochondrial membrane potential / regulation of reactive oxygen species metabolic process / regulation of canonical Wnt signaling pathway / protein K27-linked ubiquitination / response to muscle activity / positive regulation of mitochondrial fission / negative regulation of release of cytochrome c from mitochondria / response to corticosterone / dopamine metabolic process / ubiquitin-specific protease binding / Lewy body / regulation of glucose metabolic process / regulation of dopamine secretion / positive regulation of ATP biosynthetic process / cellular response to unfolded protein / regulation of protein ubiquitination / negative regulation of insulin secretion / protein monoubiquitination / cullin family protein binding / regulation of synaptic vesicle endocytosis / protein deubiquitination / mitophagy / ubiquitin ligase complex / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of postsynaptic membrane neurotransmitter receptor levels / negative regulation of mitochondrial fission / adult locomotory behavior / protein K63-linked ubiquitination / protein autoubiquitination / negative regulation of reactive oxygen species biosynthetic process / phospholipase binding / cellular response to manganese ion / heat shock protein binding / ERAD pathway / protein K48-linked ubiquitination / Hsp70 protein binding / response to endoplasmic reticulum stress / macroautophagy / positive regulation of insulin secretion involved in cellular response to glucose stimulus / central nervous system development / mitochondrion organization / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy
Similarity search - Function
: / E3 ubiquitin-protein ligase parkin / RING/Ubox-like zinc-binding domain / Parkin, RING/Ubox like zinc-binding domain / : / : / : / RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / IBR domain ...: / E3 ubiquitin-protein ligase parkin / RING/Ubox-like zinc-binding domain / Parkin, RING/Ubox like zinc-binding domain / : / : / : / RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / IBR domain / : / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMcWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. ...McWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. / Hassoun, S.M. / Mouton-Liger, F. / Ball, G. / Hills, R. / Knebel, A. / Ulusoy, A. / Di Monte, D.A. / Tamjar, J. / Antico, O. / Fears, K. / Smith, L. / Brambilla, R. / Palin, E. / Valori, M. / Eerola-Rautio, J. / Tienari, P. / Corti, O. / Dunnett, S.B. / Ganley, I.G. / Suomalainen, A. / Muqit, M.M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101022/Z/13/Z United Kingdom
CitationJournal: Open Biology / Year: 2018
Title: Phosphorylation of Parkin at serine 65 is essential for its activation in vivo .
Authors: McWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. / Hassoun, S.M. / Mouton-Liger, F. ...Authors: McWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. / Hassoun, S.M. / Mouton-Liger, F. / Ball, G. / Hills, R. / Knebel, A. / Ulusoy, A. / Di Monte, D.A. / Tamjar, J. / Antico, O. / Fears, K. / Smith, L. / Brambilla, R. / Palin, E. / Valori, M. / Eerola-Rautio, J. / Tienari, P. / Corti, O. / Dunnett, S.B. / Ganley, I.G. / Suomalainen, A. / Muqit, M.M.K.
History
DepositionOct 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.title
Revision 1.3Jan 24, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase parkin
B: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,98226
Polymers91,3042
Non-polymers1,67824
Water2,828157
1
A: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,49113
Polymers45,6521
Non-polymers83912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase parkin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,49113
Polymers45,6521
Non-polymers83912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.431, 66.870, 206.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein E3 ubiquitin-protein ligase parkin / Parkin / Parkin RBR E3 ubiquitin-protein ligase / Parkinson juvenile disease protein 2 / Parkinson ...Parkin / Parkin RBR E3 ubiquitin-protein ligase / Parkinson juvenile disease protein 2 / Parkinson disease protein 2


Mass: 45652.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKN, PARK2 / Production host: Escherichia coli (E. coli)
References: UniProt: O60260, RBR-type E3 ubiquitin transferase

-
Non-polymers , 5 types, 181 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 100mM BIS-TRIS pH 5.5, 200mM LiSO4 and 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.85→47.98 Å / Num. obs: 21291 / % possible obs: 96.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 4.5
Reflection shellResolution: 2.85→2.95 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C1Z

5c1z


Resolution: 2.85→47.98 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / SU B: 24.598 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25486 1095 5.2 %RANDOM
Rwork0.22284 ---
obs0.22449 20094 95.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.964 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2--4.08 Å20 Å2
3----5.66 Å2
Refinement stepCycle: 1 / Resolution: 2.85→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5992 0 52 159 6203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196380
X-RAY DIFFRACTIONr_bond_other_d0.0020.025847
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9448645
X-RAY DIFFRACTIONr_angle_other_deg1.0373.00813399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86323.481316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.971151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5311556
X-RAY DIFFRACTIONr_chiral_restr0.0840.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021551
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_it3.9076.4633084
X-RAY DIFFRACTIONr_mcbond_other3.9076.4633083
X-RAY DIFFRACTIONr_mcangle_it6.2739.6673847
X-RAY DIFFRACTIONr_mcangle_other6.2729.6673848
X-RAY DIFFRACTIONr_scbond_it3.6836.6683296
X-RAY DIFFRACTIONr_scbond_other3.6836.6683296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0319.8984780
X-RAY DIFFRACTIONr_long_range_B_refined11.33759.66925053
X-RAY DIFFRACTIONr_long_range_B_other11.33259.68325028
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 69 -
Rwork0.369 1425 -
obs--91.88 %

+
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