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- PDB-4om2: Crystal structure of TLE1 N-terminal Q-domain residues 1-156 -

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Basic information

Entry
Database: PDB / ID: 4om2
TitleCrystal structure of TLE1 N-terminal Q-domain residues 1-156
ComponentsTransducin-like enhancer protein 1
KeywordsTranscription / DNA binding / tetramer / helix-turn-helix / Wnt repressor / TCF/LEF
Function / homology
Function and homology information


Repression of WNT target genes / beta-catenin-TCF complex / negative regulation of Wnt signaling pathway / negative regulation of anoikis / negative regulation of canonical NF-kappaB signal transduction / Deactivation of the beta-catenin transactivating complex / animal organ morphogenesis / Formation of the beta-catenin:TCF transactivating complex / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway ...Repression of WNT target genes / beta-catenin-TCF complex / negative regulation of Wnt signaling pathway / negative regulation of anoikis / negative regulation of canonical NF-kappaB signal transduction / Deactivation of the beta-catenin transactivating complex / animal organ morphogenesis / Formation of the beta-catenin:TCF transactivating complex / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / NOTCH1 Intracellular Domain Regulates Transcription / transcription corepressor activity / DNA-binding transcription factor binding / transcription regulator complex / negative regulation of DNA-templated transcription / positive regulation of gene expression / signal transduction / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Groucho/TLE, N-terminal Q-rich domain / Groucho/TLE N-terminal Q-rich domain / Groucho/transducin-like enhancer / 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 ...Groucho/TLE, N-terminal Q-rich domain / Groucho/TLE N-terminal Q-rich domain / Groucho/transducin-like enhancer / 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
Similarity search - Domain/homology
Transducin-like enhancer protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsChodaparambil, J.V. / Weis, W.I.
CitationJournal: Embo J. / Year: 2014
Title: Molecular functions of the TLE tetramerization domain in Wnt target gene repression.
Authors: Chodaparambil, J.V. / Pate, K.T. / Hepler, M.R. / Tsai, B.P. / Muthurajan, U.M. / Luger, K. / Waterman, M.L. / Weis, W.I.
History
DepositionJan 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: Transducin-like enhancer protein 1
B: Transducin-like enhancer protein 1
C: Transducin-like enhancer protein 1
D: Transducin-like enhancer protein 1


Theoretical massNumber of molelcules
Total (without water)73,7084
Polymers73,7084
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-141 kcal/mol
Surface area29140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.586, 94.908, 130.207
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Transducin-like enhancer protein 1 / E(Sp1) homolog / Enhancer of split groucho-like protein 1 / ESG1


Mass: 18427.002 Da / Num. of mol.: 4 / Fragment: TLE Q-domain (UNP residues 1-156)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLE, TLE1 / Plasmid: pPROEX-HTB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04724
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200mM sodium thiocyanate, 15% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: MAR CCD 130 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 4→76 Å / Num. obs: 8169 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 160.69 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 4.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→53.686 Å / FOM work R set: 0.5215 / SU ML: 0.84 / σ(F): 1.14 / Phase error: 49.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3474 549 10.01 %random
Rwork0.2874 ---
obs0.2939 5484 98.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 291.08 Å2 / Biso mean: 132.2 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 4→53.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 0 0 3512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043565
X-RAY DIFFRACTIONf_angle_d0.7834799
X-RAY DIFFRACTIONf_chiral_restr0.051534
X-RAY DIFFRACTIONf_plane_restr0.003629
X-RAY DIFFRACTIONf_dihedral_angle_d17.8941355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4-4.40250.44251360.382212211357100
4.4025-5.03910.37071340.32021208134298
5.0391-6.34710.42891360.35781229136599
6.3471-53.69120.29641430.22951277142096
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5444-0.69390.73174.89261.12530.7996-1.00221.6735-0.6974-1.0156-0.9372-0.355-0.11490.2569-1.69161.5052-1.69540.63962.835-0.35890.6852-7.064.4097-24.9351
23.20220.5958-0.65090.339-0.01870.10310.6452-0.17370.4172-0.28590.4292-0.173-1.96290.27940.34011.6425-0.05620.26730.6414-0.15080.7856-16.2615-9.2995-73.3833
31.18-0.18481.49981.06750.03522.1534-1.2892.7543-1.4823-1.8010.8051-0.8541-2.098-0.2137-1.31741.5734-0.09120.32621.8961-0.4221.0283-6.7075-17.31-112.6174
41.17191.1942-0.29691.74110.10721.8278-0.126-0.69440.0495-0.4738-0.8517-1.0156-0.5091-0.6541-1.73411.12420.88060.08041.37090.02990.8511-10.46650.7373-92.1707
5-1.2633-0.0744-0.07820.051-0.30850.7335-1.04710.09060.1072-0.8109-0.21780.447-1.6655-0.2873-0.06170.969-0.1023-0.23091.3763-0.36480.6533-11.90729.530123.4879
64.24031.3258-1.3025.9866-0.49611.7450.8075-1.5063-0.24891.310.780.47960.21960.44111.8810.21730.9873-0.18620.9607-0.30520.5901-2.338415.356671.9516
70.43680.3357-0.01752.24851.92711.92770.365-0.76720.97060.75451.616-3.17610.84951.30131.0891.33140.57970.04141.48420.01481.5198-10.6451.169152.614
80.18941.2237-0.26770.72810.21711.93040.04390.20830.09710.0331-0.3589-0.0105-0.9254-0.37130.49220.73370.30510.03780.8054-0.04660.8256-13.6469-8.8588-62.9997
92.6611.1896-1.35320.5601-0.77121.2379-0.73170.3844-0.749-1.1311-0.9885-0.00170.7434-0.9069-2.61511.8468-0.1443-0.23531.655-0.43310.9685-21.7722-21.7135-103.0661
10-0.01330.72221.60850.27590.36981.6431-0.33110.72670.9181-0.5141-0.2659-0.1557-0.3955-0.0875-0.59761.04460.4202-0.33121.5465-0.67780.8686-10.099511.286822.5893
111.55150.84251.19090.40531.25758.5888-1.1093-0.58341.57370.7288-0.27660.47560.5973-3.7813-1.59180.2710.2311-1.17831.0273-0.127-1.3389-14.744725.4563.2736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 21:37)A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 38:90)A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 91:116)A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 117:132)A0
5X-RAY DIFFRACTION5CHAIN B AND (RESID 23:92)B0
6X-RAY DIFFRACTION6CHAIN B AND (RESID 93:117)B0
7X-RAY DIFFRACTION7CHAIN B AND (RESID 118:129)B0
8X-RAY DIFFRACTION8CHAIN C AND (RESID 22:92)C0
9X-RAY DIFFRACTION9CHAIN C AND (RESID 93:131)C0
10X-RAY DIFFRACTION10CHAIN D AND (RESID 22:93)D0
11X-RAY DIFFRACTION11CHAIN D AND (RESID 94:129)D0

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