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- PDB-4j2l: Crystal Structure of AXH domain complexed with Capicua -

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Basic information

Entry
Database: PDB / ID: 4j2l
TitleCrystal Structure of AXH domain complexed with Capicua
Components
  • Ataxin-1Ataxin 1
  • Protein capicua homolog
KeywordsTRANSCRIPTION REGULATOR / AXH domain / homodimerization protein-protein interaction / Capciua / ATXN1
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 / nucleolus / regulation of transcription by RNA polymerase II / 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 / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. ...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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsSong, J.-J. / Kim, E.
CitationJournal: Genes Dev. / Year: 2013
Title: Structural basis of protein complex formation and reconfiguration by polyglutamine disease protein Ataxin-1 and Capicua
Authors: Kim, E. / Lu, H.-C. / Zoghbi, H.Y. / Song, J.-J.
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,7294
Polymers34,7294
Non-polymers00
Water0
1
A: Ataxin-1
C: Protein capicua homolog


Theoretical massNumber of molelcules
Total (without water)17,3652
Polymers17,3652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-18 kcal/mol
Surface area9040 Å2
MethodPISA
2
B: Ataxin-1
D: Protein capicua homolog


Theoretical massNumber of molelcules
Total (without water)17,3652
Polymers17,3652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-18 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.500, 53.500, 276.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Ataxin-1 / Ataxin 1 / Spinocerebellar ataxia type 1 protein


Mass: 14119.982 Da / Num. of mol.: 2 / Fragment: AXH domain, UNP residues 562-688
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATXN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54253
#2: Protein/peptide Protein capicua homolog


Mass: 3244.760 Da / Num. of mol.: 2 / Fragment: UNP residues 21-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RK0

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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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6M NaCl, 3%(v/v) glycerol, 16%(w/v) PEG3350, 1mM L-Glutathione, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 8720 / % possible obs: 99.9 %
Reflection shellResolution: 3→3.05 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J2J

4j2j


Resolution: 3.15→29.23 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 107840.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.294 425 5.7 %RANDOM
Rwork0.236 ---
obs0.236 7519 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.9275 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 75.2161 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å2-0 Å2
2---2 Å2-0 Å2
3---4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 3.15→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 0 0 2302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.15→3.35 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 75 6.4 %
Rwork0.305 1103 -
all-1178 -
obs--97.5 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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