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

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Basic information

Entry
Database: PDB / ID: 4apt
TitleThe structure of the AXH domain of ataxin-1.
ComponentsATAXIN-1
KeywordsRNA BINDING PROTEIN / RNA BINDING / OB-FOLD / HIGH MOBILITY GROUP HOMOLOGY / HMG / 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 / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 5, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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)55,1305
Polymers55,1074
Non-polymers231
Water81145
1
A: ATAXIN-1
B: ATAXIN-1


Theoretical massNumber of molelcules
Total (without water)27,5532
Polymers27,5532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-36.1 kcal/mol
Surface area11750 Å2
MethodPISA
2
C: ATAXIN-1
D: ATAXIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5763
Polymers27,5532
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-42.6 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.470, 80.830, 139.960
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(0.87059, 0.4918, -0.01444), (-0.4805, 0.85615, 0.19006), (0.10584, -0.15852, 0.98167)-4.3322, -45.81432, 2.33582
2given(0.88092, 0.47311, -0.01223), (-0.46507, 0.87016, 0.16288), (0.08771, -0.1378, 0.98657)-4.24793, -45.32272, 1.57996

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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) / Plasmid: PETM30 / 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.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Description: DATA WERE MODIFIED AT THE UCLA DIFFRACTION ANISOTROPY SERVER WITH TRUNCATION ALONG D1, D2, D3 BEING 2. 90,2.50,2.50 ANGSTROMS. ALL VALUES REPORTED ARE AFTER CORRECTION, EXCEPT FOR R- ...Description: DATA WERE MODIFIED AT THE UCLA DIFFRACTION ANISOTROPY SERVER WITH TRUNCATION ALONG D1, D2, D3 BEING 2. 90,2.50,2.50 ANGSTROMS. ALL VALUES REPORTED ARE AFTER CORRECTION, EXCEPT FOR R-MERGE AND DATA REDUNDANCY WHICH ARE FOR UNCORRECTED DATA.
Crystal growDetails: PROTEIN SAMPLES AT 20 MG/ML CRYSTALLISED IN 0.4 M POTASSIUM SODIUM TARTRATE AT ROOM TEMPERATURE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→40.4 Å / Num. obs: 14350 / % possible obs: 84.4 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3 / % possible all: 35.5

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Processing

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

1oa8


Resolution: 2.5→40.406 Å / SU ML: 0.88 / σ(F): 0 / Phase error: 30.48 / 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
Rfree0.2882 729 5.1 %
Rwork0.2358 --
obs0.2385 14346 84.4 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.866 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.3005 Å20 Å20 Å2
2--3.5678 Å20 Å2
3---2.7327 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3835 0 1 45 3881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063918
X-RAY DIFFRACTIONf_angle_d0.7645316
X-RAY DIFFRACTIONf_dihedral_angle_d11.9031443
X-RAY DIFFRACTIONf_chiral_restr0.057615
X-RAY DIFFRACTIONf_plane_restr0.003687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.6930.363750.32491359X-RAY DIFFRACTION43
2.693-2.96390.38941420.32592662X-RAY DIFFRACTION84
2.9639-3.39260.33611660.27793066X-RAY DIFFRACTION97
3.3926-4.27360.2731680.21573202X-RAY DIFFRACTION99
4.2736-40.41120.24221780.19873328X-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)
12.36020.3580.01995.67670.76794.4132-0.00030.3886-0.36410.8587-0.157-0.4-0.0991-0.35920.20480.3291-0.07540.0020.30520.02660.2754-4.07550.750722.4878
23.01370.0535-1.96144.91960.34738.8483-0.53010.9663-0.1396-0.67050.58730.60430.4286-1.8740.16090.7265-0.14960.16490.97880.07630.2222-6.14612.32821.1698
33.2033-0.1155-2.13755.9877-1.80876.76250.17050.2368-0.2922-0.4757-0.2754-0.31520.1235-0.07870.22160.16220.05830.05360.20140.05110.2305-0.07384.286511.617
41.6497-1.4572-0.80154.0228-0.91274.26220.1530.38290.42540.2031-0.18480.0473-0.7456-0.85960.15280.41360.0778-0.07380.50230.00330.2278-10.539414.636619.6072
54.283-0.11451.98832.94521.30412.74420.02620.28040.2847-0.3622-0.22640.6537-0.6444-1.5561-0.10080.44310.2075-0.05540.7636-0.0170.4152-16.718714.690117.8701
61.0645-0.22430.57011.18260.31785.54630.20110.1909-0.11280.5897-0.1543-0.1746-0.38540.3031-0.59490.83910.0745-0.2820.2795-0.21440.1633-3.5928-35.257724.0456
75.87812.0313-1.31284.5112-0.00517.43030.89990.61470.3711-0.29370.27120.8598-0.1745-0.15940.50960.85970.1741-0.10570.3050.01880.3678-10.7237-42.195415.7135
83.3650.28872.15973.33150.81757.92660.09170.97120.08-0.5644-0.1055-0.10150.5081.5793-0.00580.50740.093-0.09650.6412-0.04410.2116-4.5353-40.551411.5234
91.7655-1.377-0.07854.25140.2944.6998-0.04910.24410.32380.2838-0.0874-0.45760.0910.48950.22190.66560.0419-0.19310.38510.01450.2927-2.9058-25.677623.3409
105.63570.79861.31756.9738-0.02777.8131-0.04670.5023-0.1685-0.69960.21990.23960.2145-0.2937-0.12070.4921-0.0333-0.06150.1622-0.02570.2749-13.4426-21.834213.4278
111.42860.2365-0.61617.6558-8.50179.5263-0.99570.3072-0.29240.08680.1744-1.65331.52361.5277-0.2010.694-0.1220.21250.9286-0.40160.7712.7277-23.012512.8592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN C AND (RESSEQ 565:616)
2X-RAY DIFFRACTION2CHAIN C AND (RESSEQ 617:639)
3X-RAY DIFFRACTION3CHAIN C AND (RESSEQ 640:689)
4X-RAY DIFFRACTION4CHAIN D AND (RESSEQ 565:632)
5X-RAY DIFFRACTION5CHAIN D AND (RESSEQ 633:688)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 565:595)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 596:625)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 626:689)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 565:607)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 608:683)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 684:689)

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