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- PDB-4bte: DJ-1 Cu(I) complex -

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Basic information

Entry
Database: PDB / ID: 4bte
TitleDJ-1 Cu(I) complex
ComponentsPROTEIN DJ-1
KeywordsHYDROLASE / COPPER CHAPERONE / PARKINSON'S DISEASE / SUPEROXIDE DISMUTASE ACTIVATION / MULTI-FUNCTIONAL
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 / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization ...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 / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal removal / 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 L-dopa biosynthetic process / 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 / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / methylglyoxal metabolic process / detoxification of mercury ion / ubiquitin-protein transferase inhibitor activity / protein deglycase / mercury ion binding / protein deglycase activity / hydrogen peroxide metabolic process / positive regulation of dopamine biosynthetic process / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of mitochondrial electron transport, NADH to ubiquinone / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / lactate biosynthetic process / protein repair / peptidase inhibitor activity / cellular detoxification of aldehyde / peroxiredoxin activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / small protein activating enzyme binding / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / detoxification of copper ion / negative regulation of protein sumoylation / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein export from nucleus / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cupric ion binding / regulation of androgen receptor signaling pathway / membrane hyperpolarization / oxygen sensor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / insulin secretion / ubiquitin-like protein conjugating enzyme binding / nuclear androgen receptor binding / androgen receptor signaling pathway / ubiquitin-specific protease binding / dopamine uptake involved in synaptic transmission / cytokine binding / positive regulation of reactive oxygen species biosynthetic process / cuprous ion binding / signaling receptor activator activity / membrane depolarization / regulation of synaptic vesicle endocytosis / single fertilization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / removal of superoxide radicals / SUMOylation of transcription cofactors / adult locomotory behavior / 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 / enzyme activator activity / Late endosomal microautophagy / PML body / mitochondrial intermembrane space / autophagy / positive regulation of protein localization to nucleus / kinase binding / cellular response to hydrogen peroxide / Chaperone Mediated Autophagy / positive regulation of reactive oxygen species metabolic process / Aggrephagy / synaptic vesicle / glucose homeostasis / peptidase activity / cell body / cellular response to oxidative stress / response to oxidative stress / regulation of inflammatory response / scaffold protein binding / DNA-binding transcription factor 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
COPPER (I) ION / Parkinson disease protein 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsPuno, M.R.A. / Odell, M. / Moody, P.C.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Structure of Cu(I)-Bound Dj-1 Reveals a Biscysteinate Metal Binding Site at the Homodimer Interface: Insights Into Mutational Inactivation of Dj-1 in Parkinsonism.
Authors: Puno, M.R. / Patel, N.A. / Moller, S.G. / Robinson, C.V. / Moody, P.C.E. / Odell, M.
History
DepositionJun 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9812
Polymers19,9171
Non-polymers641
Water3,927218
1
A: PROTEIN DJ-1
hetero molecules

A: PROTEIN DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9614
Polymers39,8342
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2890 Å2
ΔGint-35.8 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.257, 75.257, 75.354
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1189-

CU1

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Components

#1: Protein PROTEIN DJ-1 / DJ-1 / ONCOGENE DJ1 / PARKINSON DISEASE PROTEIN 7


Mass: 19917.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q99497, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 61 % / Description: CU ANOMALOUS OPTIMISED

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.3772
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3772 Å / Relative weight: 1
ReflectionResolution: 1.38→26.2 Å / Num. obs: 46017 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 28.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.8
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.1 / % possible all: 15.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PDV

1pdv


Resolution: 1.38→26.64 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.127 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES HAVE BEEN REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14981 2343 5.1 %RANDOM
Rwork0.11841 ---
obs0.11996 43643 89.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.11 Å20 Å2
2--0.11 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.38→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 1 218 1594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191412
X-RAY DIFFRACTIONr_bond_other_d0.0020.021437
X-RAY DIFFRACTIONr_angle_refined_deg2.1831.9961911
X-RAY DIFFRACTIONr_angle_other_deg1.0443.0013321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13625.4951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10715258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.439157
X-RAY DIFFRACTIONr_chiral_restr0.1480.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.70632848
X-RAY DIFFRACTIONr_sphericity_free55.546592
X-RAY DIFFRACTIONr_sphericity_bonded13.34152955
LS refinement shellResolution: 1.378→1.414 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 47 -
Rwork0.278 818 -
obs--22.91 %

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