[English] 日本語
Yorodumi
- PDB-3b1l: Crystal Structure of parkin ubiquitin-like domain R33Q mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b1l
TitleCrystal Structure of parkin ubiquitin-like domain R33Q mutant
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / Parkin / Ubiquitin / proteasome / Alfa-Beta-protein
Function / homology
Function and homology information


positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / cellular response to L-glutamine / negative regulation of exosomal secretion ...positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / cellular response to L-glutamine / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / Regulation of necroptotic cell death / Aggrephagy / type 2 mitophagy / response to curcumin / cellular response to hydrogen sulfide / negative regulation of mitochondrial fusion / Parkin-FBXW7-Cul1 ubiquitin ligase complex / free ubiquitin chain polymerization / positive regulation of protein linear polyubiquitination / negative regulation of actin filament bundle assembly / host-mediated suppression of viral genome replication / RBR-type E3 ubiquitin transferase / F-box domain binding / positive regulation of mitochondrial fusion / regulation of cellular response to oxidative stress / mitochondrial fragmentation involved in apoptotic process / mitochondrion localization / regulation of dopamine metabolic process / positive regulation of dendrite extension / negative regulation of excitatory postsynaptic potential / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of neurotransmitter secretion / protein K6-linked ubiquitination / dopaminergic synapse / norepinephrine metabolic process / autophagy of mitochondrion / positive regulation of type 2 mitophagy / protein localization to mitochondrion / cellular response to L-glutamate / synaptic transmission, dopaminergic / positive regulation of protein localization to membrane / cellular response to toxic substance / mitochondrial fission / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / aggresome assembly / protein K11-linked ubiquitination / negative regulation of synaptic transmission, glutamatergic / regulation of mitochondrion organization / ubiquitin conjugating enzyme binding / positive regulation of mitochondrial membrane potential / negative regulation of JNK cascade / aggresome / response to corticosterone / positive regulation of mitochondrial fission / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / response to muscle activity / negative regulation of release of cytochrome c from mitochondria / startle response / dopamine metabolic process / positive regulation of ATP biosynthetic process / cullin family protein binding / protein K63-linked ubiquitination / regulation of synaptic vesicle endocytosis / protein monoubiquitination / cellular response to manganese ion / negative regulation of mitochondrial fission / response to unfolded protein / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of postsynaptic membrane neurotransmitter receptor levels / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / phospholipase binding / mitophagy / protein autoubiquitination / negative regulation of reactive oxygen species biosynthetic process / regulation of mitochondrial membrane potential / Hsp70 protein binding / tubulin binding / response to endoplasmic reticulum stress / adult locomotory behavior / ubiquitin binding / learning / mitochondrion organization / synaptic transmission, glutamatergic / PDZ domain binding / locomotory behavior / protein catabolic process / G protein-coupled receptor binding / negative regulation of insulin secretion / negative regulation of canonical Wnt signaling pathway / protein destabilization / modulation of chemical synaptic transmission / beta-catenin binding / kinase binding / histone deacetylase binding / neuron cellular homeostasis
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTomoo, K. / Ikemiya, A. / Amami, Y. / In, Y. / Ishida, T.
CitationJournal: to be published
Title: Crystal Structure of parkin ubiquitin-like domain R33Q mutant
Authors: Tomoo, K. / Ikemiya, A. / Amami, Y. / In, Y. / Ishida, T.
History
DepositionJul 4, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: E3 ubiquitin-protein ligase parkin


Theoretical massNumber of molelcules
Total (without water)8,7011
Polymers8,7011
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.790, 45.790, 65.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein E3 ubiquitin-protein ligase parkin


Mass: 8700.982 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain / Mutation: R33Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WVS6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3M NaCl, 100mM acetate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→33.99 Å / Num. all: 6738 / Num. obs: 6718 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.42 % / Rmerge(I) obs: 0.079

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→25.36 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.979 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 320 4.8 %RANDOM
Rwork0.1885 ---
obs0.1908 6708 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.43 Å2 / Biso mean: 17.9307 Å2 / Biso min: 7.71 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 0 33 645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022622
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.957842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.559575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23624.06332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97415112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.413156
X-RAY DIFFRACTIONr_chiral_restr0.1480.297
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021474
X-RAY DIFFRACTIONr_mcbond_it1.2041.5381
X-RAY DIFFRACTIONr_mcangle_it2.1762625
X-RAY DIFFRACTIONr_scbond_it4.0343241
X-RAY DIFFRACTIONr_scangle_it6.8964.5217
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 27 -
Rwork0.25 464 -
all-491 -
obs--99.8 %

+
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