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- PDB-6glc: Structure of phospho-Parkin bound to phospho-ubiquitin -

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Basic information

Entry
Database: PDB / ID: 6glc
TitleStructure of phospho-Parkin bound to phospho-ubiquitin
Components
  • E3 ubiquitin-protein ligase parkin
  • Polyubiquitin-B
KeywordsLIGASE / ubiquitin / Parkin / phospho-ubiquitin / Parkinson's disease / E3 ligase / RBR domain / mitophagy
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 / regulation of protein targeting to mitochondrion / 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 / regulation of protein targeting to mitochondrion / negative regulation of exosomal secretion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / Lewy body / negative regulation of actin filament bundle assembly / protein K27-linked ubiquitination / negative regulation of mitochondrial fusion / Parkin-FBXW7-Cul1 ubiquitin ligase complex / protein K29-linked ubiquitination / free ubiquitin chain polymerization / positive regulation of protein linear polyubiquitination / negative regulation by host of viral genome replication / positive regulation of mitophagy / RBR-type E3 ubiquitin transferase / regulation of synaptic vesicle transport / F-box domain binding / positive regulation of mitochondrial fusion / regulation of cellular response to oxidative stress / regulation of necroptotic process / regulation of dopamine metabolic process / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / dopaminergic synapse / positive regulation of dendrite extension / protein K6-linked ubiquitination / positive regulation of protein localization to membrane / autophagy of mitochondrion / norepinephrine metabolic process / cellular response to toxic substance / positive regulation of type 2 mitophagy / protein localization to mitochondrion / positive regulation of proteasomal protein catabolic process / cellular response to dopamine / negative regulation of JNK cascade / mitochondrial fission / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / aggresome assembly / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / hypothalamus gonadotrophin-releasing hormone neuron development / regulation of canonical Wnt signaling pathway / female meiosis I / aggresome / positive regulation of protein monoubiquitination / regulation of reactive oxygen species metabolic process / fat pad development / mitochondrion transport along microtubule / positive regulation of mitochondrial fission / female gonad development / dopamine uptake involved in synaptic transmission / seminiferous tubule development / ubiquitin-specific protease binding / negative regulation of release of cytochrome c from mitochondria / regulation of dopamine secretion / startle response / dopamine metabolic process / male meiosis I / phospholipase binding / regulation of synaptic vesicle endocytosis / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of glucose metabolic process / protein K63-linked ubiquitination / protein deubiquitination / protein monoubiquitination / regulation of protein ubiquitination / cellular response to manganese ion / ubiquitin ligase complex / cellular response to unfolded protein / negative regulation of insulin secretion / proteasomal protein catabolic process / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein autoubiquitination / mitophagy / energy homeostasis / regulation of neuron apoptotic process / ERAD pathway / heat shock protein binding / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway
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 domain signature. / Ubiquitin conserved site / Ubiquitin domain / 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 / Polyubiquitin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGladkova, C. / Maslen, S.L. / Skehel, J.M. / Komander, D.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council309756 United Kingdom
European Research Council724804 United Kingdom
Michael J. Fox Foundation United Kingdom
CitationJournal: Nature / Year: 2018
Title: Mechanism of parkin activation by PINK1.
Authors: Gladkova, C. / Maslen, S.L. / Skehel, J.M. / Komander, D.
History
DepositionMay 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 16, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,53213
Polymers51,6492
Non-polymers88311
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-42 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.931, 83.931, 105.119
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-228-

HOH

21B-231-

HOH

31B-233-

HOH

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Components

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Protein , 2 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: 43008.551 Da / Num. of mol.: 1
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
#2: Protein Polyubiquitin-B


Mass: 8640.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 5 types, 176 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.03 M of each sodium nitrate, disodium hydrogen phosphate, ammonium sulphate, 0.1 M MOPS/HEPES-Na (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 1.8→72.69 Å / Num. obs: 40324 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.8
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2339 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5n2w, 5c1z

5n2w

5c1z


Resolution: 1.8→59.786 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 22.14
RfactorNum. reflection% reflection
Rfree0.2054 2020 5.02 %
Rwork0.1799 --
obs0.1812 40229 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→59.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 37 165 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073135
X-RAY DIFFRACTIONf_angle_d0.8634255
X-RAY DIFFRACTIONf_dihedral_angle_d9.9412600
X-RAY DIFFRACTIONf_chiral_restr0.056483
X-RAY DIFFRACTIONf_plane_restr0.005550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.84510.29581420.28052683X-RAY DIFFRACTION100
1.8451-1.8950.29491490.26252708X-RAY DIFFRACTION100
1.895-1.95070.26491410.23182734X-RAY DIFFRACTION100
1.9507-2.01370.24871480.21322657X-RAY DIFFRACTION100
2.0137-2.08570.2751560.21112658X-RAY DIFFRACTION100
2.0857-2.16920.25131430.20262708X-RAY DIFFRACTION100
2.1692-2.26790.23381320.18832740X-RAY DIFFRACTION100
2.2679-2.38750.22091410.1892711X-RAY DIFFRACTION100
2.3875-2.53710.26151650.20022693X-RAY DIFFRACTION100
2.5371-2.7330.24331380.18922720X-RAY DIFFRACTION100
2.733-3.0080.22811280.19682746X-RAY DIFFRACTION100
3.008-3.44320.19391260.18162776X-RAY DIFFRACTION100
3.4432-4.33790.17331400.14932790X-RAY DIFFRACTION100
4.3379-59.81880.15811710.15622885X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -6.6329 Å / Origin y: -26.8647 Å / Origin z: -16.2338 Å
111213212223313233
T0.1784 Å2-0.0097 Å20.0429 Å2-0.2594 Å20.0543 Å2--0.2549 Å2
L0.8967 °2-0.1595 °20.6828 °2-1.1407 °20.2808 °2--2.0369 °2
S0.0639 Å °0.244 Å °0.122 Å °-0.0855 Å °-0.0894 Å °-0.1474 Å °-0.2512 Å °0.1791 Å °0.0308 Å °
Refinement TLS groupSelection details: all

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