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- PDB-4wth: Ataxin-3 Carboxy Terminal Region - Crystal C2 (triclinic) -

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Basic information

Entry
Database: PDB / ID: 4wth
TitleAtaxin-3 Carboxy Terminal Region - Crystal C2 (triclinic)
ComponentsMaltose-binding periplasmic protein, Ataxin-3 chimera
KeywordsTRANSCRIPTION / ataxin-3 / polyglutamine helix / nerve tissue proteins / polyQ / triplet repeat disorder
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 / nuclear inclusion body / protein K48-linked deubiquitination / positive regulation of ubiquitin-dependent protein catabolic process / K48-linked deubiquitinase activity / 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 / nuclear inclusion body / protein K48-linked deubiquitination / positive regulation of ubiquitin-dependent protein catabolic process / K48-linked deubiquitinase activity / cellular response to misfolded protein / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / detection of maltose stimulus / maltose transport complex / exploration behavior / carbohydrate transport / protein quality control for misfolded or incompletely synthesized proteins / carbohydrate transmembrane transporter activity / protein deubiquitination / maltose binding / maltose transport / maltodextrin transmembrane transport / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of TORC1 signaling / ATP-binding cassette (ABC) transporter complex / cellular response to amino acid starvation / Josephin domain DUBs / cell chemotaxis / nucleotide-excision repair / mitochondrial membrane / microtubule cytoskeleton organization / nuclear matrix / 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 / periplasmic space / mitochondrial matrix / lysosomal membrane / DNA damage response / synapse / ubiquitin protein ligase binding / nucleolus / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Machado-Joseph disease protein / Unstructured region C-term to UIM in Ataxin3 / Josephin domain / Josephin / Josephin domain profile. / Josephin / Ubiquitin interaction motif / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. ...Machado-Joseph disease protein / Unstructured region C-term to UIM in Ataxin3 / 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 / 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: 2.25 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
National Ataxia FoundationTranslational Award United States
Russian Ministry of Science and Education17.1360.2014/K Russian Federation
Russian Scientific Fund14-25-00024 Russian Federation
Russian Ministry of Science and Education11.G34.31.0056 Russian Federation
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
DepositionOct 30, 2014Deposition 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 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 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_assembly_gen / pdbx_struct_conn_angle / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_asym.entity_id
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
A: Maltose-binding periplasmic protein, Ataxin-3 chimera
B: Maltose-binding periplasmic protein, Ataxin-3 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,23010
Polymers97,1532
Non-polymers1,0778
Water2,684149
1
A: Maltose-binding periplasmic protein, Ataxin-3 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1155
Polymers48,5761
Non-polymers5394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltose-binding periplasmic protein, Ataxin-3 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1155
Polymers48,5761
Non-polymers5394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.096, 59.786, 77.790
Angle α, β, γ (deg.)90.00, 89.99, 87.50
Int Tables number1
Space group name H-MP1

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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.: 2
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, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% PEG5000 MME, 0.9 M sodium acetate, 0.06 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: Oct 10, 2010
RadiationMonochromator: Rosenbaum-Rock high-resolution 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: 2.25→38.743 Å / Num. all: 41971 / Num. obs: 39115 / % possible obs: 94 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.7
Reflection shellResolution: 2.25→2.36 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.2 / % possible all: 76

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Processing

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

1anf


Resolution: 2.25→77.79 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.067 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24975 1980 5.1 %RANDOM
Rwork0.20187 ---
obs0.20424 37158 93.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å21.18 Å2-0.31 Å2
2---1.64 Å2-0.21 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.25→77.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 52 149 6462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026457
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9648753
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3115807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58725.973293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.927151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6641516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214912
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: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.554 113 -
Rwork0.563 2105 -
obs--70.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
147.2701-24.234113.250412.4799-6.78213.71922.04780.77580.9255-1.6085-1.4719-0.36580.77830.1384-0.57591.08440.362-0.3131.6222-0.06380.6974-49.66646.225719.1978
220.9436-3.57923.17998.93093.492.4426-0.2636-0.476-0.92310.71570.8178-0.5960.29870.3683-0.55420.57720.00790.00130.8713-0.05720.6217-11.6849-32.819659.3678
34.69082.24131.57366.3772-0.1924.10620.0303-0.30290.22440.2526-0.05810.4818-0.1233-0.35640.02780.11330.04320.04910.10920.00010.0471-41.9239-4.938618.2323
44.2561.5404-0.98054.99580.38893.78160.1298-0.1781-0.26230.4291-0.1101-0.52240.03770.3199-0.01970.11840.0313-0.04950.10250.01430.0577-18.031-21.763557.0968
51.4096-0.2084-0.16083.00720.15330.97550.02310.0696-0.1534-0.0807-0.00980.12210.0463-0.0692-0.01330.0439-0.0091-0.00130.07-0.00420.0222-36.7929-20.43986.2329
61.3934-0.22860.13692.8456-0.04530.9420.01430.07250.1524-0.09-0.0072-0.0777-0.0620.0793-0.00710.0549-0.00310.01010.06990.00960.019-23.188-6.262545.1168
74.0560.17170.6522.57730.08791.40190.04420.0401-0.2542-0.1817-0.03290.27260.1259-0.2059-0.01130.09890.0177-0.01670.0699-0.00340.049-43.4203-24.9443.0502
83.48120.1143-0.53231.9154-0.51351.54740.0135-0.15080.2697-0.2569-0.0533-0.2055-0.11170.1980.03980.1040.02130.04260.0926-0.00940.0611-16.5124-1.731541.9617
923.733-4.214111.96465.4206-3.76519.23270.21910.569-0.0116-0.2529-0.07030.18150.07880.0991-0.14880.1870.03010.03610.16-0.03210.0332-78.3099-14.8206-9.9559
1025.2523-5.7806-12.59255.3764.89449.59820.37310.92790.0315-0.3904-0.2851-0.2058-0.2934-0.1635-0.08810.20040.0252-0.00870.15980.05630.043618.3243-11.877528.922
1124.11369.2448-27.65333.5451-10.60131.7138-1.05111.11040.3235-0.59810.88870.16891.7675-1.28930.16231.38340.522-0.30491.0671-0.79062.643-101.6478-3.3585-17.7695
1218.51739.6306-8.68125.0094-4.52054.1795-1.08731.37361.839-0.78371.21550.96470.3717-0.9216-0.12821.68920.7939-0.43481.7346-0.05551.929537.9347-25.005311.737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION2B1 - 6
3X-RAY DIFFRACTION3A7 - 56
4X-RAY DIFFRACTION4B7 - 56
5X-RAY DIFFRACTION5A57 - 308
6X-RAY DIFFRACTION6B57 - 308
7X-RAY DIFFRACTION7A309 - 370
8X-RAY DIFFRACTION8B309 - 370
9X-RAY DIFFRACTION9A371 - 397
10X-RAY DIFFRACTION10B371 - 397
11X-RAY DIFFRACTION11A398 - 403
12X-RAY DIFFRACTION12B398 - 406

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