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- PDB-2xte: Structure of the TBL1 tetramerisation domain -

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Basic information

Entry
Database: PDB / ID: 2xte
TitleStructure of the TBL1 tetramerisation domain
ComponentsF-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / Notch-HLH transcription pathway / histone deacetylase complex / Regulation of MECP2 expression and activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) ...Loss of MECP2 binding ability to the NCoR/SMRT complex / Notch-HLH transcription pathway / histone deacetylase complex / Regulation of MECP2 expression and activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / HDACs deacetylate histones / sensory perception of sound / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / Circadian Clock / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / transcription cis-regulatory region binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
F-box-like/WD repeat-containing protein Ebi-like / Mitochondrial Import Receptor Subunit Tom20; Chain A - #30 / LisH / Lissencephaly type-1-like homology motif / Mitochondrial Import Receptor Subunit Tom20; Chain A / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...F-box-like/WD repeat-containing protein Ebi-like / Mitochondrial Import Receptor Subunit Tom20; Chain A - #30 / LisH / Lissencephaly type-1-like homology motif / Mitochondrial Import Receptor Subunit Tom20; Chain A / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
F-box-like/WD repeat-containing protein TBL1X
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.9 Å
AuthorsOberoi, J. / Fairall, L. / Watson, P.J. / Greenwood, J.A. / Schwabe, J.W.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural Basis for the Assembly of the Smrt/Ncor Core Transcriptional Repression Machinery.
Authors: Oberoi, J. / Fairall, L. / Watson, P.J. / Yang, J.C. / Czimmerer, Z. / Kampmann, T. / Goult, B.T. / Greenwood, J.A. / Gooch, J.T. / Kallenberger, B.C. / Nagy, L. / Neuhaus, D. / Schwabe, J.W.R.
History
DepositionOct 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
B: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
C: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
D: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
E: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
F: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
G: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
H: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
I: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
J: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
K: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
L: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X


Theoretical massNumber of molelcules
Total (without water)118,09112
Polymers118,09112
Non-polymers00
Water0
1
A: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
B: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
I: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
J: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X


Theoretical massNumber of molelcules
Total (without water)39,3644
Polymers39,3644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-58.9 kcal/mol
Surface area14560 Å2
MethodPISA
2
C: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
D: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
K: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
L: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X


Theoretical massNumber of molelcules
Total (without water)39,3644
Polymers39,3644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-57.5 kcal/mol
Surface area14660 Å2
MethodPISA
3
E: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
F: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
G: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
H: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X


Theoretical massNumber of molelcules
Total (without water)39,3644
Polymers39,3644
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-58.8 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.020, 150.190, 164.830
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
F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X / TRANSDUCIN BETA-LIKE PROTEIN 1X / TBL1 / TRANSDUCIN-BETA-LIKE PROTEIN1\ / X-LINKED / SMAP55


Mass: 9840.949 Da / Num. of mol.: 12 / Fragment: N-TERMINAL TETRAMERISATION DOMAIN, RESIDUES 1-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60907

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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: 4.61 Å3/Da / Density % sol: 73.34 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M MES PH6.5, 2.0 M NACL, 0.175 M SODIUM ACETATE, 19 % GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.972
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 3.9→111.1 Å / Num. obs: 19503 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.1
Reflection shellResolution: 3.9→4.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 2XTC

2xtc


Resolution: 3.9→111.1 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1023 5 %RANDOM
Rwork0.273 ---
obs0.273 20526 99.8 %-
Solvent computationBsol: 75.24 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 101 Å2
Baniso -1Baniso -2Baniso -3
1-17.944 Å20 Å20 Å2
2--13.749 Å20 Å2
3----31.693 Å2
Refinement stepCycle: LAST / Resolution: 3.9→111.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 0 0 0 6036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.24
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM

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