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- PDB-4j2j: Crystal structure of AXH domain complex with Capicua -

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Basic information

Entry
Database: PDB / ID: 4j2j
TitleCrystal structure of AXH domain complex with Capicua
Components
  • Ataxin-1
  • Protein capicua homolog
KeywordsTRANSCRIPTION REGULATOR / AXH domain / protein-protein interaction / Capicua
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 / 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 / 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 / SAD / Resolution: 2.5 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

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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: Protein capicua homolog
E: Protein capicua homolog
F: Protein capicua homolog


Theoretical massNumber of molelcules
Total (without water)49,9906
Polymers49,9906
Non-polymers00
Water50428
1
A: Ataxin-1
D: Protein capicua homolog


Theoretical massNumber of molelcules
Total (without water)16,6632
Polymers16,6632
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-20 kcal/mol
Surface area7480 Å2
MethodPISA
2
B: Ataxin-1
E: Protein capicua homolog


Theoretical massNumber of molelcules
Total (without water)16,6632
Polymers16,6632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-20 kcal/mol
Surface area7780 Å2
MethodPISA
3
C: Ataxin-1
F: Protein capicua homolog


Theoretical massNumber of molelcules
Total (without water)16,6632
Polymers16,6632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-19 kcal/mol
Surface area7230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.722, 89.096, 132.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 14296.744 Da / Num. of mol.: 3 / Fragment: AXH domain, UNP residues 562-688 / Mutation: I580M,I605M
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: 2366.712 Da / Num. of mol.: 3 / Fragment: UNP residues 28-48
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.45 % / Description: THE FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Calcium chloride, 24%(v/v) PEG3350, 4%(v/v) pentaerythritol ethoxylate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32436 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 52.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 15 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 5.43 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→43.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 65239.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THE FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1494 5 %RANDOM
Rwork0.223 ---
obs0.223 29785 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.7754 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 57.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å2-0 Å20 Å2
2--6.67 Å20 Å2
3----7.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 0 28 3161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 228 5 %
Rwork0.313 4313 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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