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- PDB-4aqp: The structure of the AXH domain of ataxin-1. -

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Basic information

Entry
Database: PDB / ID: 4aqp
TitleThe structure of the AXH domain of ataxin-1.
ComponentsATAXIN-1
KeywordsRNA BINDING PROTEIN / OB-FOLD / HIGH MOBILITY GROUP HOMOLOGY / HMG
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
DI(HYDROXYETHYL)ETHER / Ataxin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.452 Å
AuthorsRees, M. / Chen, Y.W. / de Chiara, C. / Pastore, A.
Citation
Journal: Biophys.J. / Year: 2013
Title: Self-Assembly and Conformational Heterogeneity of the Axh Domain of Ataxin-1: An Unusual Example of a Chameleon Fold
Authors: De Chiara, C. / Rees, M. / Menon, R.P. / Pauwels, K. / Lawrence, C. / Konarev, P.V. / Svergun, D.I. / Martin, S.R. / Chen, Y.W. / Pastore, A.
#1: 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.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 2005
Title: Polyglutamine is not All: The Functional Role of the Axh Domain in the Ataxin-1 Protein.
Authors: De Chiara, C. / Menon, R.P. / Dal Piaz, F. / Calder, L. / Pastore, A.
History
DepositionApr 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 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 / pdbx_struct_conn_angle / 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 / _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.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_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.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_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

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)55,2828
Polymers55,1074
Non-polymers1754
Water1,15364
1
A: ATAXIN-1
B: ATAXIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6824
Polymers27,5532
Non-polymers1292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-44.3 kcal/mol
Surface area11790 Å2
MethodPISA
2
C: ATAXIN-1
D: ATAXIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5994
Polymers27,5532
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-53.2 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.539, 82.699, 137.110
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(0.8823, 0.4589, 0.10466), (-0.47068, 0.86009, 0.19673), (0.00026, -0.22283, 0.97486)-7.0637, -46.59366, 2.88887
2given(0.85773, 0.49449, 0.14065), (-0.51254, 0.8438, 0.15906), (-0.04002, -0.20852, 0.9772)-8.26149, -46.12433, 2.19498

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Components

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


Mass: 13776.670 Da / Num. of mol.: 4 / Fragment: AXH DOMAIN, RESIDUES 566-688
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) / Variant (production host): PLYSS / References: UniProt: P54253
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Description: DATA WERE MODIFIED AT THE UCLA DIFFRACTION ANISOTROPY SERVER WITH TRUNCATION ALONG D1, D2, D3 BEING 2.90,2.45,2.45 ANGSTROMS. ALL VALUES REPORTED ARE AFTER CORRECTION, EXCEPT FOR R-MERGE ...Description: DATA WERE MODIFIED AT THE UCLA DIFFRACTION ANISOTROPY SERVER WITH TRUNCATION ALONG D1, D2, D3 BEING 2.90,2.45,2.45 ANGSTROMS. ALL VALUES REPORTED ARE AFTER CORRECTION, EXCEPT FOR R-MERGE AND DATA REDUNDANCY WHICH IS FOR UNCORRECTED DATA.
Crystal growpH: 6.5
Details: PROTEIN SAMPLES AT 20 MG/ML CRYSTALLISED IN 0.1 M MES, PH 6.5, 10% W/V PWG 20000 AT ROOM TEMPERATURE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9697
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9697 Å / Relative weight: 1
ReflectionResolution: 2.45→70.9 Å / Num. obs: 16989 / % possible obs: 82.7 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 47.71 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.8
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 4.5 / % possible all: 32.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OA8

1oa8


Resolution: 2.452→44.916 Å / SU ML: 0.78 / σ(F): 1.38 / Phase error: 29.95 / Stereochemistry target values: ML
Details: THERE ARE 4 CHEMICALLY IDENTICAL PROTEIN MOLECULES IN THE ASYMMETRIC UNIT. CHAINS A AND B CONSTITUTE A GLOBULAR DIMER, C & D FORM ANOTHER. CHAINS A AND B ARE STRUCTURALLY SLIGHTLY DIFFERENT, ...Details: THERE ARE 4 CHEMICALLY IDENTICAL PROTEIN MOLECULES IN THE ASYMMETRIC UNIT. CHAINS A AND B CONSTITUTE A GLOBULAR DIMER, C & D FORM ANOTHER. CHAINS A AND B ARE STRUCTURALLY SLIGHTLY DIFFERENT, LIKEWISE FOR C & D CHAINS. A AND C ARE MORE ALIKE AND SO ARE CHAINS B & D. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.2672 856 5 %
Rwork0.2175 --
obs0.2201 16984 82.7 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.331 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 53.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.7993 Å20 Å20 Å2
2--1.3985 Å20 Å2
3---0.4007 Å2
Refinement stepCycle: LAST / Resolution: 2.452→44.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 10 64 3918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083946
X-RAY DIFFRACTIONf_angle_d0.7235352
X-RAY DIFFRACTIONf_dihedral_angle_d13.7141451
X-RAY DIFFRACTIONf_chiral_restr0.05616
X-RAY DIFFRACTIONf_plane_restr0.004690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.452-2.60560.4943510.31651134X-RAY DIFFRACTION35
2.6056-2.80680.34321140.29182192X-RAY DIFFRACTION68
2.8068-3.08920.3031500.2793040X-RAY DIFFRACTION95
3.0892-3.5360.28891850.24813168X-RAY DIFFRACTION99
3.536-4.45440.24441700.19353228X-RAY DIFFRACTION99
4.4544-44.92330.24091860.1843366X-RAY DIFFRACTION98
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)
12.85982.17252.44092.33222.04953.60280.37670.5012-0.46690.313-0.2173-0.01480.0381.07460.07970.39030.1303-0.10440.4485-0.14070.2479-5.0027.358320.9089
21.2001-0.2941-0.68012.8918-1.2453.97070.08510.0749-0.0118-0.2122-0.0436-0.03560.0251-0.13960.02790.11320.030.13910.0866-0.07850.1368-2.42081.436811.4699
32.01490.10311.09625.50050.79384.5-0.1074-0.07290.2688-0.1093-0.10350.2766-0.3043-0.3630.16710.27330.0665-0.07990.15-0.06490.1737-13.293514.809817.5979
44.28050.262.93183.2597-0.81454.26380.1326-0.0004-0.3790.8002-0.12820.15530.51490.0747-0.15810.57680.0048-0.07380.1209-0.12130.24-5.3434-34.503922.8276
52.81560.39421.57763.96321.12383.67070.1665-0.2008-0.28470.00640.219-0.17810.60780.0386-0.23610.290.042-0.11490.1363-0.03950.2046-7.4217-42.012313.2768
62.0212-0.57732.63023.6613.19767.9372-0.1883-0.06630.2330.1317-0.0031-0.3646-0.123-0.06540.23350.2767-0.025-0.01360.13050.0540.1877-6.9504-31.116422.9227
73.57860.99511.12815.59640.15364.6054-0.11450.07030.092-0.1396-0.0150.1654-0.2275-0.01960.11820.14370.0405-0.02930.2072-0.06150.1933-10.8739-22.210215.0508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN C AND (RESSEQ 564:587)
2X-RAY DIFFRACTION2CHAIN C AND (RESSEQ 588:689)
3X-RAY DIFFRACTION3CHAIN D AND (RESSEQ 565:689)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 565:589)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 590:689)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 564:591)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 592:689)

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