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- PDB-2m41: Solution Structure of the AXH domain of Ataxin-1 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2m41
TitleSolution Structure of the AXH domain of Ataxin-1 in complex with ligand peptide from Capicua
Components
  • Ataxin-1
  • Protein capicua homolog
KeywordsTRANSCRIPTION REGULATOR / protein/protein / Ataxin-1 AXH-CIC complex
Function / homology
Function and homology information


poly(G) binding / nuclear inclusion body / nuclear export / poly(U) RNA binding / social behavior / RNA processing / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory ...poly(G) binding / nuclear inclusion body / nuclear export / poly(U) RNA binding / social behavior / RNA processing / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory / nuclear matrix / nervous system development / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / 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 / Domain of unknown function DUF4819 / ATAXIN1-like / Ataxin-1 like family / Domain of unknown function (DUF4819) / : / Ataxin, AXH domain / Ataxin, AXH domain superfamily / Ataxin-1 and HBP1 module (AXH) / AXH domain profile. ...Ataxin-1, N-terminal / Domain of unknown function DUF4819 / ATAXIN1-like / Ataxin-1 like family / Domain of unknown function (DUF4819) / : / Ataxin, AXH domain / Ataxin, AXH domain superfamily / Ataxin-1 and HBP1 module (AXH) / AXH domain profile. / domain in Ataxins and HMG containing proteins / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
Ataxin-1 / Protein capicua homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model19
Authorsde Chiara, C. / Kelly, G. / Pastore, A.
Citation
Journal: Plos One / Year: 2013
Title: Protein-Protein Interactions as a Strategy towards Protein-Specific Drug Design: The Example of Ataxin-1.
Authors: de Chiara, C. / Menon, R.P. / Kelly, G. / Pastore, A.
#2: Journal: To be Published
Title: 1H,13C, and 15N resonance assignment of the ataxin-1 AXH domain in complex with CIC ligand peptide
Authors: de Chiara, C. / Kelly, G. / Pastore, A.
History
DepositionJan 28, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein capicua homolog
B: Ataxin-1


Theoretical massNumber of molelcules
Total (without water)15,5032
Polymers15,5032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Protein capicua homolog


Mass: 1726.003 Da / Num. of mol.: 1 / Fragment: Ataxin-1-binding linear motif (UNP 34-48) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96RK0
#2: Protein Ataxin-1 / Spinocerebellar ataxia type 1 protein


Mass: 13776.670 Da / Num. of mol.: 1 / Fragment: AXH domain, native residues A567-K689
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATXN1, ATX1, SCA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54253

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-15N NOESY
1223D 1H-15N TOCSY
1313D 1H-13C NOESY
1413D (H)CCH-TOCSY
1513D CBCA(CO)NH
1613D HNCA
1713D HNCO
1813D 15N-13C-filtered, 15N-13C-edited NOESY
1912D 15N-13C-rejected NOESY
11013D C(CO)NH
11113D HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] Ataxin-1 AXH domain, 0.6 mM CIC polypeptide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 15N] Ataxin-1 AXH domain, 0.6 mM CIC polypeptide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAtaxin-1 AXH domain-1[U-100% 13C; U-100% 15N]1
0.6 mMCIC polypeptide-21
0.5 mMAtaxin-1 AXH domain-3[U-100% 15N]2
0.6 mMCIC polypeptide-42
Sample conditionsIonic strength: 20 / pH: 6.8 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesautomated noes assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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