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

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Basic information

Entry
Database: PDB / ID: 2xtc
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 / sensory perception of sound / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian expression / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression ...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 / sensory perception of sound / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian expression / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / Activation of gene expression by SREBF (SREBP) / transcription repressor complex / Heme signaling / HDACs deacetylate histones / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / HCMV Early Events / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / histone binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription cis-regulatory region binding / protein stabilization / 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
Mitochondrial Import Receptor Subunit Tom20; Chain A - #30 / F-box-like/WD repeat-containing protein Ebi-like / LisH / Mitochondrial Import Receptor Subunit Tom20; Chain A / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #30 / F-box-like/WD repeat-containing protein Ebi-like / LisH / Mitochondrial Import Receptor Subunit Tom20; Chain A / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / 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 / MOLECULAR REPLACEMENT / Resolution: 2.22 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


Theoretical massNumber of molelcules
Total (without water)19,6822
Polymers19,6822
Non-polymers00
Water77543
1
A: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
B: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X

A: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
B: F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X


Theoretical massNumber of molelcules
Total (without water)39,3644
Polymers39,3644
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6430 Å2
ΔGint-57.1 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.541, 59.541, 193.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-2009-

HOH

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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.: 2 / 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.52 Å3/Da / Density % sol: 51.2 % / Description: NONE
Crystal growpH: 7.4
Details: 17% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS/HCL PH8.5, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→96 Å / Num. obs: 10905 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UUJ

1uuj


Resolution: 2.22→51.57 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.423 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26437 523 5 %RANDOM
Rwork0.23723 ---
obs0.23854 10313 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.44 Å20 Å2
2--0.89 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.22→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 0 43 1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221063
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9421445
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.255135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65815161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.739152
X-RAY DIFFRACTIONr_chiral_restr0.1260.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02807
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.2458
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2757
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8581.5690
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34421082
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6293399
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5874.5362
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.216→2.274 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 40 -
Rwork0.261 727 -
obs--100 %

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