+Open data
-Basic information
Entry | Database: PDB / ID: 2xte | ||||||
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Title | Structure of the TBL1 tetramerisation domain | ||||||
Components | F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X | ||||||
Keywords | TRANSCRIPTION | ||||||
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 / Transcriptional regulation of white adipocyte differentiation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / HCMV Early Events / transcription corepressor activity / positive regulation of canonical Wnt signaling pathway / Circadian Clock / histone binding / 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 | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.9 Å | ||||||
Authors | Oberoi, J. / Fairall, L. / Watson, P.J. / Greenwood, J.A. / Schwabe, J.W.R. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xte.cif.gz | 156.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xte.ent.gz | 127.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xte.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xte_validation.pdf.gz | 520 KB | Display | wwPDB validaton report |
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Full document | 2xte_full_validation.pdf.gz | 541.8 KB | Display | |
Data in XML | 2xte_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 2xte_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/2xte ftp://data.pdbj.org/pub/pdb/validation_reports/xt/2xte | HTTPS FTP |
-Related structure data
Related structure data | 2l5gC 2xtcSC 2xtdC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.61 Å3/Da / Density % sol: 73.34 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M MES PH6.5, 2.0 M NACL, 0.175 M SODIUM ACETATE, 19 % GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.972 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.9→4.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 2XTC Resolution: 3.9→111.1 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 75.24 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 101 Å2
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Refinement step | Cycle: LAST / Resolution: 3.9→111.1 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM |