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- PDB-4lg9: Crystal structure of TBL1XR1 WD40 repeats -

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Basic information

Entry
Database: PDB / ID: 4lg9
TitleCrystal structure of TBL1XR1 WD40 repeats
ComponentsF-box-like/WD repeat-containing protein TBL1XR1
KeywordsUNKNOWN FUNCTION / Structural Genomics Consortium / SGC / WD40 repeats
Function / homology
Function and homology information


regulation of triglyceride metabolic process / Loss of MECP2 binding ability to the NCoR/SMRT complex / blastocyst hatching / fat pad development / Notch-HLH transcription pathway / response to dietary excess / white fat cell differentiation / histone deacetylase complex / Regulation of MECP2 expression and activity / lipid catabolic process ...regulation of triglyceride metabolic process / Loss of MECP2 binding ability to the NCoR/SMRT complex / blastocyst hatching / fat pad development / Notch-HLH transcription pathway / response to dietary excess / white fat cell differentiation / histone deacetylase complex / Regulation of MECP2 expression and activity / lipid catabolic process / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / : / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / HDACs deacetylate histones / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / multicellular organism growth / Transcriptional regulation of white adipocyte differentiation / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / HCMV Early Events / transcription corepressor activity / mitotic spindle / positive regulation of canonical Wnt signaling pathway / : / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 / nucleoplasm / nucleus
Similarity search - Function
F-box-like/WD repeat-containing protein Ebi-like / LisH / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...F-box-like/WD repeat-containing protein Ebi-like / LisH / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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 / Mainly Beta
Similarity search - Domain/homology
F-box-like/WD repeat-containing protein TBL1XR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsXu, C. / Tempel, W. / He, H. / Wu, X. / Seitova, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of TBL1XR1 WD40 repeats
Authors: Xu, C. / Tempel, W. / He, H. / Wu, X. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Structure summary
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F-box-like/WD repeat-containing protein TBL1XR1


Theoretical massNumber of molelcules
Total (without water)43,64924
Polymers43,6491
Non-polymers023
Water2,882160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.776, 90.776, 104.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsAUTHORS STATE THAT THe BIOLOGICAL MOLECULE IS UNKNOWN.

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Components

#1: Protein F-box-like/WD repeat-containing protein TBL1XR1 / Nuclear receptor corepressor/HDAC3 complex subunit TBLR1 / TBL1-related protein 1 / Transducin beta- ...Nuclear receptor corepressor/HDAC3 complex subunit TBLR1 / TBL1-related protein 1 / Transducin beta-like 1X-related protein 1


Mass: 43649.469 Da / Num. of mol.: 1 / Fragment: UNP residues 134-514 / Mutation: L438M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBL1XR1, IRA1, TBLR1 / Plasmid: pFBOH-LIC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q9BZK7
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 23 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growMethod: vapor diffusion / Details: vapor diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.93→78.614 Å / Num. obs: 23135 / % possible obs: 100 % / Redundancy: 9.3 % / Rsym value: 0.149 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.93-2.036.50.9790.80.9791100
2.03-2.166.50.5871.30.5871100
2.16-2.316.70.1484.20.148199.8
2.31-2.4911.40.3462.20.3461100
2.49-2.7311.40.25530.2551100
2.73-3.0511.40.1624.80.1621100
3.05-3.5211.40.0938.10.0931100
3.52-4.3210.70.0885.70.0881100
4.32-6.111.10.05113.70.0511100
6.1-45.38810.50.05113.30.051199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PHASERphasing
PHENIXdev_1439refinement
PDB_EXTRACT3.12data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ymu, ensemble of triple repeats (345-467, 102-225)

2ymu


Resolution: 2.28→45.388 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.23 / σ(F): 0.15 / Phase error: 19.63 / Stereochemistry target values: ML
Details: ARP/WARP, REFMAC, COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT. RESOLUTION WAS LIMITED TO 2.28A DUE TO THE PRESENCE OF STRONG ICE RINGS ON DIFFRACTION IMAGES. UNMERGED ...Details: ARP/WARP, REFMAC, COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT. RESOLUTION WAS LIMITED TO 2.28A DUE TO THE PRESENCE OF STRONG ICE RINGS ON DIFFRACTION IMAGES. UNMERGED INTENSITIES TO 1.93A RESOLUTION ARE ALSO PROVIDED. DENSITY FOR RESIDUE 270 DOES NOT MATCH PHENYLALANYL TYPE.
RfactorNum. reflection% reflection
Rfree0.2081 2270 5.18 %
Rwork0.1632 --
obs0.1656 23135 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.4511 Å2
Refinement stepCycle: LAST / Resolution: 2.28→45.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 23 160 2855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072812
X-RAY DIFFRACTIONf_angle_d1.1493845
X-RAY DIFFRACTIONf_dihedral_angle_d12.272993
X-RAY DIFFRACTIONf_chiral_restr0.046429
X-RAY DIFFRACTIONf_plane_restr0.005495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.32960.24921370.18062600X-RAY DIFFRACTION100
2.3296-2.38380.21231230.16442665X-RAY DIFFRACTION100
2.3838-2.44340.1971510.15062559X-RAY DIFFRACTION100
2.4434-2.50940.21761370.15542597X-RAY DIFFRACTION100
2.5094-2.58330.21881490.16142636X-RAY DIFFRACTION100
2.5833-2.66660.21091500.16332611X-RAY DIFFRACTION100
2.6666-2.76190.22791280.1692628X-RAY DIFFRACTION100
2.7619-2.87250.24861490.17422584X-RAY DIFFRACTION100
2.8725-3.00320.22841730.16942597X-RAY DIFFRACTION100
3.0032-3.16150.21781320.17432614X-RAY DIFFRACTION100
3.1615-3.35950.22461390.17272631X-RAY DIFFRACTION100
3.3595-3.61880.21051650.16182568X-RAY DIFFRACTION100
3.6188-3.98280.25561230.18322385X-RAY DIFFRACTION91
3.9828-4.55870.16051620.12782603X-RAY DIFFRACTION100
4.5587-5.74160.1631370.13892624X-RAY DIFFRACTION100
5.7416-45.39680.1671150.18572643X-RAY DIFFRACTION100

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