[English] 日本語
Yorodumi
- PDB-4zgg: Crystal structure of a DJ-1 (PARK7) from Homo sapiens at 1.23 A r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zgg
TitleCrystal structure of a DJ-1 (PARK7) from Homo sapiens at 1.23 A resolution
ComponentsProtein deglycase DJ-1
KeywordsCHAPERONE / Parkinson disease / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / Partnership for Nuclear Receptor Signaling Code Biology / NHRs / Partnership for T-Cell Biology / TCELL / PSI-BIOLOGY
Function / homology
Function and homology information


positive regulation of acute inflammatory response to antigenic stimulus / tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / detoxification of hydrogen peroxide / detection of oxidative stress / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway ...positive regulation of acute inflammatory response to antigenic stimulus / tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / detoxification of hydrogen peroxide / detection of oxidative stress / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / glycolate biosynthetic process / glyoxal metabolic process / detoxification of mercury ion / ubiquitin-protein transferase inhibitor activity / hydrogen peroxide metabolic process / protein deglycase / mercury ion binding / methylglyoxal metabolic process / superoxide dismutase copper chaperone activity / protein deglycase activity / positive regulation of autophagy of mitochondrion / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of dopamine biosynthetic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / lactate biosynthetic process / protein repair / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / peroxiredoxin activity / peptidase inhibitor activity / cellular detoxification of aldehyde / small protein activating enzyme binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / detoxification of copper ion / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / androgen receptor signaling pathway / negative regulation of protein export from nucleus / negative regulation of protein sumoylation / cupric ion binding / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of androgen receptor signaling pathway / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / oxygen sensor activity / nuclear androgen receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / ubiquitin-specific protease binding / cytokine binding / response to testosterone / cuprous ion binding / signaling receptor activator activity / regulation of synaptic vesicle endocytosis / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / removal of superoxide radicals / negative regulation of protein ubiquitination / SUMOylation of transcription cofactors / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of neuron apoptotic process / regulation of mitochondrial membrane potential / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / mitochondrion organization / adherens junction / positive regulation of protein-containing complex assembly / positive regulation of protein localization to nucleus / Late endosomal microautophagy / mitochondrial intermembrane space / PML body / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / kinase binding / enzyme activator activity / Chaperone Mediated Autophagy / Aggrephagy / peptidase activity / glucose homeostasis / synaptic vesicle / negative regulation of neuron apoptotic process / regulation of inflammatory response / cellular response to oxidative stress / response to oxidative stress / cell body / scaffold protein binding / DNA-binding transcription factor binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Ras protein signal transduction / transcription coactivator activity / protein stabilization / cadherin binding / membrane raft / mitochondrial matrix / copper ion binding / negative regulation of gene expression / DNA repair / signaling receptor binding
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / : / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.23 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Nuclear Receptor Signaling Code Biology (NHRS) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a DJ-1 (PARK7) from Homo sapiens at 1.23 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Nuclear Receptor Signaling Code Biology (NHRs) / Partnership for T-Cell Biology (TCELL)
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references / Structure summary
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: audit_author / entity_src_gen ...audit_author / entity_src_gen / pdbx_struct_oper_list / software
Item: _audit_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Feb 1, 2023Group: Data collection / Database references
Category: database_2 / diffrn_radiation_wavelength / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,82911
Polymers20,2091
Non-polymers62110
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein deglycase DJ-1
hetero molecules

A: Protein deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,65922
Polymers40,4172
Non-polymers1,24120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6200 Å2
ΔGint30 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.002, 75.002, 74.897
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Protein deglycase DJ-1 / DJ-1 / Oncogene DJ1 / Parkinson disease protein 7


Mass: 20208.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1
References: UniProt: Q99497, Hydrolases; Acting on ester bonds; Thioester hydrolases, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 5.00% polyethylene glycol 6000, 0.1M TRIS pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 6, 2014
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.23→29.796 Å / Num. all: 69760 / Num. obs: 69760 / % possible obs: 98.3 % / Redundancy: 6.9 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.124 / Rsym value: 0.115 / Net I/av σ(I): 3.912 / Net I/σ(I): 8.1 / Num. measured all: 479140
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.23-1.264.10.9130.8040.91848244730.4220.9130.80411.786.1
1.26-1.35.10.7550.6791.12334346080.3240.7550.6792.291.6
1.3-1.336.50.6260.5771.33174048600.2420.6260.5772.999
1.33-1.387.10.530.4911.53428047970.1970.530.4913.5100
1.38-1.427.20.4470.4151.83355846720.1660.4470.4154.1100
1.42-1.477.20.3650.3382.23259345160.1350.3650.3384.8100
1.47-1.537.20.2980.2772.73137643340.110.2980.2775.6100
1.53-1.597.30.2580.243.13008541410.0960.2580.246.4100
1.59-1.667.30.2230.2073.52963640630.0820.2230.2077.4100
1.66-1.747.30.1920.17842802238320.070.1920.1788.3100
1.74-1.837.30.1690.1574.42685736620.0620.1690.1579.6100
1.83-1.947.30.1480.1384.92546734740.0550.1480.13811100
1.94-2.087.40.1380.1285.12415432840.050.1380.12812.8100
2.08-2.257.40.1230.1145.72227230270.0450.1230.11414.4100
2.25-2.467.40.110.1026.52097128410.040.110.10215.5100
2.46-2.757.40.1090.1016.41872625440.040.1090.10116.3100
2.75-3.187.30.1070.16.51661422690.0390.1070.117.3100
3.18-3.897.30.0810.0758.41421819500.030.0810.07518.9100
3.89-5.57.20.0730.0689.31092915280.0270.0730.06819.2100
5.5-29.7966.60.0870.088.258178850.0330.0870.0817.198.9

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMAC5.8.0103refinement
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.23→29.796 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.931 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.027
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4. EDO MODELED WAS PRESENT IN CRYO CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1339 3374 4.8 %RANDOM
Rwork0.1164 66326 --
obs0.1172 69700 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.57 Å2 / Biso mean: 17.4434 Å2 / Biso min: 7.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å2-0 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.23→29.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 40 198 1634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221557
X-RAY DIFFRACTIONr_bond_other_d0.0030.021631
X-RAY DIFFRACTIONr_angle_refined_deg1.6972.0092100
X-RAY DIFFRACTIONr_angle_other_deg1.09133785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15725.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47415298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.353158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211745
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02297
X-RAY DIFFRACTIONr_mcbond_it2.0642.409801
X-RAY DIFFRACTIONr_mcbond_other1.9922.402800
X-RAY DIFFRACTIONr_mcangle_it2.0344.5421009
X-RAY DIFFRACTIONr_rigid_bond_restr2.71733187
X-RAY DIFFRACTIONr_sphericity_free30.1295129
X-RAY DIFFRACTIONr_sphericity_bonded8.77353237
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 192 -
Rwork0.287 4272 -
all-4464 -
obs--85.71 %

+
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