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

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Basic information

Entry
Database: PDB / ID: 2xtd
TitleStructure of the TBL1 tetramerisation domain
ComponentsTBL1 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
KeywordsTRANSCRIPTION / N-COR REPRESSOR COMPLEX / PROTEASOME
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 / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / transcription corepressor activity / positive regulation of canonical Wnt signaling pathway / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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: 3.2 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: TBL1 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
B: TBL1 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X


Theoretical massNumber of molelcules
Total (without water)15,5672
Polymers15,5672
Non-polymers00
Water00
1
A: TBL1 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
B: TBL1 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X

A: TBL1 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X
B: TBL1 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X


Theoretical massNumber of molelcules
Total (without water)31,1344
Polymers31,1344
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_654-x+y+1,y,-z-1/31
Buried area6770 Å2
ΔGint-60.4 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.886, 47.886, 153.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A53 - 119
2115B53 - 119

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Components

#1: Protein TBL1 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X / TRANSDUCIN BETA-LIKE PROTEIN 1X / TBL1 / TRANSDUCIN -BETA-LIKE PROTEIN1\ / X-LINKED / SMAP55


Mass: 7783.602 Da / Num. of mol.: 2 / Fragment: N-TERMINAL TETRAMERISATION DOMAIN, RESIDUES 1-71
Source method: isolated from a genetically manipulated source
Details: ISOFORM 2 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60907
Sequence detailsTBL1X ISOFORM B, UNIPROT ISOFORM 2.

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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: 3.27 Å3/Da / Density % sol: 62.39 % / Description: NONE
Crystal growpH: 4.5 / Details: 15% MPD, 0.05 M SODIUM ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.2→51 Å / Num. obs: 3503 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.2
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.1 / % 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 2XTC

2xtc


Resolution: 3.2→51.3 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.846 / Cross valid method: THROUGHOUT / ESU R: 1.674 / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.3153 162 4.6 %RANDOM
Rwork0.2783 ---
obs0.28001 3339 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å21.32 Å20 Å2
2--2.64 Å20 Å2
3----3.96 Å2
Refinement stepCycle: LAST / Resolution: 3.2→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 0 0 1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0221034
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.9431405
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3715130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.78325.31947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.4315162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.478152
X-RAY DIFFRACTIONr_chiral_restr0.1420.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02782
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.2485
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2780.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A48medium positional0.140.5
2B48medium positional0.140.5
1A42loose positional0.725
2B42loose positional0.725
LS refinement shellResolution: 3.202→3.285 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 13 -
Rwork0.334 218 -
obs--100 %

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