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- PDB-1ow1: Crystal structure of the SPOC domain of the human transcriptional... -

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Basic information

Entry
Database: PDB / ID: 1ow1
TitleCrystal structure of the SPOC domain of the human transcriptional corepressor, SHARP.
ComponentsSMART/HDAC1 associated repressor protein
KeywordsTRANSCRIPTION / beta-alpha-barrel / SPOC domain
Function / homology
Function and homology information


RHOBTB1 GTPase cycle / positive regulation of neurogenesis / Notch signaling pathway / transcription repressor complex / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / mRNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II ...RHOBTB1 GTPase cycle / positive regulation of neurogenesis / Notch signaling pathway / transcription repressor complex / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / mRNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
SHARP, RNA recognition motif 1 / SHARP, RNA recognition motif 2 / SHARP, RNA recognition motif 3 / SHARP, RNA recognition motif 4 / : / : / : / Msx2-interacting protein, RAM7 domain / Msx2-interacting protein, MID domain / Msx2-interacting protein, nuclear receptor-interacting domain ...SHARP, RNA recognition motif 1 / SHARP, RNA recognition motif 2 / SHARP, RNA recognition motif 3 / SHARP, RNA recognition motif 4 / : / : / : / Msx2-interacting protein, RAM7 domain / Msx2-interacting protein, MID domain / Msx2-interacting protein, nuclear receptor-interacting domain / Spen paralogue/orthologue C-terminal, metazoa / SPOC domain profile. / Ku70; Chain: A; Domain 2 - #10 / Ku70; Chain: A; Domain 2 / Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / SPOC-like, C-terminal domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Msx2-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsSchwabe, J.W. / Ariyoshi, M.
CitationJournal: Genes Dev. / Year: 2003
Title: A conserved structural motif reveals the essential transcriptional repression function of Spen proteins and their role in developmental signaling
Authors: Schwabe, J.W. / Ariyoshi, M.
History
DepositionMar 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SMART/HDAC1 associated repressor protein


Theoretical massNumber of molelcules
Total (without water)21,3261
Polymers21,3261
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.300, 61.980, 68.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SMART/HDAC1 associated repressor protein / Msx2 interacting nuclear target (MINT) homolog


Mass: 21325.590 Da / Num. of mol.: 1 / Fragment: SPOC domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta BL21(DE3) pLysS / References: UniProt: Q96T58
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.29 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 4000, glycerol, Tris-HCl, NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris-HCl1reservoirpH7.5
230 %PEG40001reservoir
35 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 16853 / Num. obs: 16853 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.7 Å2 / Rsym value: 0.068 / Net I/σ(I): 17.1
Reflection shellResolution: 1.8→1.84 Å / Num. unique all: 1103 / Rsym value: 0.082 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 258694 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 5.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 1201298.27 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1674 10 %RANDOM
Rwork0.214 ---
all0.214 16731 --
obs0.214 16731 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9783 Å2 / ksol: 0.389495 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å20 Å2
2--4.21 Å20 Å2
3----1.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.06 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 0 82 1368
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 261 9.7 %
Rwork0.201 2430 -
obs-2430 97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Highest resolution: 1.8 Å

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