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- PDB-4ys9: Ataxin-3 Carboxy-Terminal Region - Crystal C1 (tetragonal) -

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Basic information

Entry
Database: PDB / ID: 4ys9
TitleAtaxin-3 Carboxy-Terminal Region - Crystal C1 (tetragonal)
ComponentsMaltose-binding periplasmic protein, Ataxin-3 chimera
KeywordsTRANSCRIPTION / Ataxin-3 / Polyglutamine / Huntington's Disease / Triplet repeat disorder / ataxins / ataxia
Function / homology
Function and homology information


protein localization to cytosolic proteasome complex / regulation of cell-substrate adhesion / positive regulation of ERAD pathway / monoubiquitinated protein deubiquitination / intermediate filament cytoskeleton organization / protein K48-linked deubiquitination / nuclear inclusion body / positive regulation of ubiquitin-dependent protein catabolic process / protein K63-linked deubiquitination / cellular response to misfolded protein ...protein localization to cytosolic proteasome complex / regulation of cell-substrate adhesion / positive regulation of ERAD pathway / monoubiquitinated protein deubiquitination / intermediate filament cytoskeleton organization / protein K48-linked deubiquitination / nuclear inclusion body / positive regulation of ubiquitin-dependent protein catabolic process / protein K63-linked deubiquitination / cellular response to misfolded protein / K48-linked deubiquitinase activity / exploration behavior / K63-linked deubiquitinase activity / protein quality control for misfolded or incompletely synthesized proteins / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of TORC1 signaling / cellular response to amino acid starvation / Josephin domain DUBs / nucleotide-excision repair / mitochondrial membrane / nuclear matrix / microtubule cytoskeleton organization / nervous system development / cellular response to heat / outer membrane-bounded periplasmic space / ATPase binding / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / chemical synaptic transmission / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mitochondrial matrix / lysosomal membrane / synapse / ubiquitin protein ligase binding / nucleolus / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Unstructured region C-term to UIM in Ataxin3 / Machado-Joseph disease protein / Josephin domain / Josephin / Josephin domain profile. / Josephin / Ubiquitin interaction motif / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. ...Unstructured region C-term to UIM in Ataxin3 / Machado-Joseph disease protein / Josephin domain / Josephin / Josephin domain profile. / Josephin / Ubiquitin interaction motif / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Ataxin-3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhemkov, V.A. / Kim, M.
Funding support United States, Russian Federation, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS074376 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS056224 United States
Russian Ministry of Science11.G34.31.0056 Russian Federation
Russian Scientific Fund14-25-00024 Russian Federation
Russian Ministry of Education and Science17.1360.2014/K Russian Federation
National Ataxia FoundationTranslational Award United States
CitationJournal: FEBS Open Bio / Year: 2016
Title: The 2.2-Angstrom resolution crystal structure of the carboxy-terminal region of ataxin-3.
Authors: Zhemkov, V.A. / Kulminskaya, A.A. / Bezprozvanny, I.B. / Kim, M.
History
DepositionMar 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Maltose-binding periplasmic protein, Ataxin-3 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1806
Polymers48,5761
Non-polymers6045
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-100 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.670, 59.670, 135.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Maltose-binding periplasmic protein, Ataxin-3 chimera / MBP / MMBP / Maltodextrin-binding protein / Machado-Joseph disease protein 1 / Spinocerebellar ...MBP / MMBP / Maltodextrin-binding protein / Machado-Joseph disease protein 1 / Spinocerebellar ataxia type 3 protein


Mass: 48576.438 Da / Num. of mol.: 1
Fragment: MBP residues 27-392 (UNP) + Ataxin-3 C-terminal region (UNP residues 278-324)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, ATXN3, ATX3, MJD, MJD1, SCA3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEY0, UniProt: P54252
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 25% PEG5000 MME, 1.0 M sodium acetate, 0.1 M imidazole, pH 8.0, 0.1 M zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→44.7 Å / Num. all: 31801 / Num. obs: 31801 / % possible obs: 99.8 % / Redundancy: 1.9 % / Rsym value: 0.053 / Net I/σ(I): 23.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.2 / % possible all: 58

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data collection
HKL-2000data scaling
Cootmodel building
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ANF

1anf


Resolution: 2→59.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.921 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22327 1607 5.1 %RANDOM
Rwork0.20735 ---
obs0.20819 30210 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.834 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2→59.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 27 90 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.023070
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9531.974168
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6755383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93825.564133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56615510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.514158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212322
X-RAY DIFFRACTIONr_gen_planes_other
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 124 -
Rwork0.271 2205 -
obs--100 %

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