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- PDB-1oa8: AXH domain of human spinocerebellar ataxin-1 -

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Basic information

Entry
Database: PDB / ID: 1oa8
TitleAXH domain of human spinocerebellar ataxin-1
ComponentsATAXIN-1
KeywordsRNA BINDING / HIGH MOBILITY GROUP HOMOLOGY / HMG / RNA-BINDING / DIMERIZATION
Function / homology
Function and homology information


poly(G) binding / nuclear inclusion body / nuclear export / poly(U) RNA binding / social behavior / RNA processing / learning / brain development / memory / nuclear matrix ...poly(G) binding / nuclear inclusion body / nuclear export / poly(U) RNA binding / social behavior / RNA processing / learning / brain development / memory / nuclear matrix / nervous system development / negative regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ataxin-1, N-terminal / ATAXIN1-like / Ataxin-1 like family / Ataxin, AXH domain / Ataxin, AXH domain superfamily / Ataxin-1 and HBP1 module (AXH) / AXH domain profile. / domain in Ataxins and HMG containing proteins
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsAllen, M.D. / Chen, Y.W. / Bycroft, M.
Citation
Journal: J. Biol. Chem. / Year: 2004
Title: The structure of the AXH domain of spinocerebellar ataxin-1.
Authors: Chen, Y.W. / Allen, M.D. / Veprintsev, D.B. / Lowe, J. / Bycroft, M.
#1: Journal: FEBS Lett. / Year: 2003
Title: The Axh Module: An Independently Folded Domain Common to Ataxin-1 and Hbp1.
Authors: De Chiara, C. / Giannini, C. / Adinolfi, S. / De Boer, J. / Guida, S. / Ramos, A. / Jodice, C. / Kioussis, D. / Pastore, A.
History
DepositionJan 2, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Feb 6, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Oct 9, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.6May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATAXIN-1
B: ATAXIN-1
C: ATAXIN-1
D: ATAXIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7827
Polymers57,7134
Non-polymers693
Water6,810378
1
A: ATAXIN-1
B: ATAXIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8803
Polymers28,8572
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATAXIN-1
D: ATAXIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9034
Polymers28,8572
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.783, 82.441, 137.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.66921, -0.05497, 0.74103), (0.09155, -0.99576, 0.00882), (0.73741, 0.07374, 0.67141)-27.01102, -63.26282, 14.60991
2given(0.87622, -0.48188, -0.00465), (0.4707, 0.85787, -0.20614), (0.10332, 0.17844, 0.97851)-15.61538, 43.61203, 5.62488
3given(-0.6656, 0.38544, 0.63907), (-0.35225, -0.91718, 0.1863), (0.65795, -0.10111, 0.74624)-11.01075, -27.62694, 5.62451

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Components

#1: Protein
ATAXIN-1 / SPINOCEREBELLAR ATAXIA TYPE 1 PROTEIN


Mass: 14428.339 Da / Num. of mol.: 4 / Fragment: AXH DOMAIN, RESIDUES 562-694
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P54253
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Compound detailsATAXIN-1 BINDS TO RNA IN VITRO.

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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: 2.37 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M TRIS/HCL, PH 7.0, 0.2M AMMONIUM SULPHATE, 5 MM DTT, 15% PEG 4000, 20% GLYCEROL, AT 290K
Crystal grow
*PLUS
Temperature: 290 K / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium citrate1reservoirpH5.8
20.1 Mammonium sulfate1reservoir
35 mMdithiothreitol1reservoir
416 %PEG40001reservoir
520 %glycerol1reservoir
620 mg/mlprotein1drop
710 mMTris1droppH7.0
85 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.960,0.97916,0.97966
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961
20.979161
30.979661
ReflectionResolution: 1.7→70.71 Å / Num. obs: 62044 / % possible obs: 99.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 5.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.7 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 70.7 Å / Redundancy: 4.3 % / Num. measured all: 267655 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 98.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→70.71 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.883 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: DISORDERED REGION IN B CHAIN (RESIDUES 39 - 51) MODELED BUILT FROM SE-METHONINE DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3125 5.1 %RANDOM
Rwork0.21 ---
obs-58574 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å20 Å2
2---1.09 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 3 378 4315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214018
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9715458
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1230.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21747
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2347
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1760.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2921.52585
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.25324201
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.33331433
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.644.51257
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 224
Rwork0.274 4211
Refinement
*PLUS
Lowest resolution: 70.7 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.78

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