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- PDB-4om3: Crystal structure of human TLE1 Q-domain residues 20-156 -

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Basic information

Entry
Database: PDB / ID: 4om3
TitleCrystal structure of human TLE1 Q-domain residues 20-156
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 / NOTCH1 Intracellular Domain Regulates Transcription ...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 / NOTCH1 Intracellular Domain Regulates Transcription / Wnt signaling pathway / 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 / MIR / Resolution: 2.855 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7926
Polymers66,6084
Non-polymers1842
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14330 Å2
ΔGint-163 kcal/mol
Surface area30030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.687, 89.678, 130.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 16652.016 Da / Num. of mol.: 4 / Fragment: TLE Q-domain (UNP residues 15-156)
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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M HEPES pH 7.0 or 7.5, 15% Tacsimate pH 7.0, 10% PEG 3350, 10% 2-methyl, 2,4-pentanediol (MPD) and 100mM RbCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-211.03
SYNCHROTRONSSRL BL12-220.97
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.031
20.971
ReflectionResolution: 2.8→40 Å / Num. obs: 11004 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 57.97 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.855→39.104 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 31.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2976 548 4.98 %
Rwork0.2335 --
obs0.2369 11004 77.78 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.1 Å2
Refinement stepCycle: LAST / Resolution: 2.855→39.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 12 0 3764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043821
X-RAY DIFFRACTIONf_angle_d0.7635139
X-RAY DIFFRACTIONf_dihedral_angle_d13.9211442
X-RAY DIFFRACTIONf_chiral_restr0.054568
X-RAY DIFFRACTIONf_plane_restr0.005672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.855-3.14230.3891590.3221014X-RAY DIFFRACTION31
3.1423-3.59670.38071500.28742942X-RAY DIFFRACTION88
3.5967-4.53040.28761560.21133235X-RAY DIFFRACTION96
4.5304-39.10770.25941830.2173265X-RAY DIFFRACTION94
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)
11.00732.05924.64072.05892.04312.0173-1.22210.86921.6887-2.3542-0.81170.41740.1747-3.0471.2581.47111.2474-1.28671.66141.8839-1.76726.42716.240687.7317
25.5244-2.69355.5167.2981-8.35492.51650.4460.57160.8599-1.1366-1.8036-0.86911.64881.26991.14150.97520.08770.10370.62510.13550.76314.7641-1.7913119.8501
32.04419.0886-1.64989.4443-8.62682.0155-0.95440.3627-0.101-1.6934-0.16741.19651.3108-3.11691.70671.8532-0.2197-0.02561.38330.24410.69957.8413-2.92584.871
45.9895-1.1597-0.08650.84421.47243.91060.6244-0.505-1.3217-0.5814-1.0827-0.57732.7339-0.366-0.04432.1648-0.4048-0.21821.18340.23040.797812.72080.876463.9361
52.1311-3.58620.61462.8819-6.84152.6609-1.1101-0.70260.34851.3094-0.1429-0.8102-1.8621-0.25271.01121.3075-0.2676-0.27930.73420.04460.644313.586814.648721.6365
69.14034.9604-9.00586.3254-7.07112.3049-0.34970.4286-0.7026-0.82560.0693-0.19240.8241-0.41520.53431.13630.11540.11291.0234-0.02230.600616.5087-4.102595.405
79.58683.0557-1.96671.7667-4.0062.0614-0.56490.43220.0487-1.5988-0.2006-0.01720.80231.49040.72531.31540.0233-0.00750.67960.09550.497811.5664-10.5914122.2444
85.2279-2.2861-0.19924.9592-1.68152.1948-0.0764-0.0604-0.06640.3041-0.24870.1832-0.7612-0.790.17170.3551-0.0475-0.03070.431-0.07550.4519.875-12.0195151.2403
92.05330.26350.43485.0066-7.58232.088-0.6926-0.12910.83610.43640.11980.5082-0.0174-1.11550.90021.2225-0.184-0.27930.90640.05330.734916.63218.194385.1108
107.9617-1.4437.15515.0121-0.44452.07950.32110.12080.7107-0.4614-0.60240.0715-0.6909-2.65021.06021.53040.0389-0.19331.46270.12210.677711.047510.415267.8618
116.9723-3.3462-1.24948.8032-2.55182.3756-0.4714-0.0507-0.73371.1771-0.4524-0.4204-0.8151.0120.92920.5362-0.1185-0.09370.5524-0.04650.582115.9747-18.3247155.8557
124.22231.8048-3.70510.7222-1.61068.1641-1.3077-1.2334-1.81882.6878-0.32171.29970.8397-0.93171.13842.43240.23720.4831.17550.22320.85356.3293-18.2922177.9995
132.25686.95453.70372.7368-7.53612.8712-1.53011.8817-0.32280.09840.7985-1.4571-1.21230.48621.21991.1565-0.18480.16070.7453-0.1880.973612.89210.7584157.0228
146.6191-2.405-1.21627.7999-3.42312.6021.77262.0657-0.9718-1.0575-2.91912.322-0.4415-2.9741-0.05280.2156-0.64030.14170.15390.14511.05444.384811.853-6.8248
152.5029-2.17240.59851.615-0.31231.5739-0.3677-0.56540.9471-1.11340.4486-0.77380.46730.13560.23991.4876-0.5360.02651.05090.22311.645914.9061-1.205913.2761
163.5658-0.768-4.09731.2647-0.88148.5304-1.1745-1.65930.29732.4772-0.0573-0.15330.95161.82910.95421.84960.553-0.15571.4363-0.03390.874620.1257-21.1266172.1825
172.09031.81892.57962.0782-2.53672.06312.0433-1.11973.87171.9016-1.79183.19031.4285-1.3085-0.22290.9303-0.03220.17850.8975-0.04251.17746.1881-33.454150.301
182.12940.56841.68262.1634-0.59852.2432-0.0558-1.01480.02820.55190.4144-0.035-0.6347-0.2151-0.51460.9507-0.012-0.20761.04670.07220.67758.259910.54334.1941
193.3922-0.72631.9316.07420.19552.62880.03290.0740.33160.5209-0.2898-0.3086-0.36021.19890.20520.6954-0.29830.0060.58490.09580.767317.270817.5162-3.2158
202.4288-0.7042-2.22580.07980.27751.7792-0.8899-1.23241.4879-0.3848-0.15980.7635-0.3141-0.74280.52122.3136-0.45390.15460.83420.06141.38149.842725.286422.6511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 20:32)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 33:64 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 21: 32 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 33:49 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 50:93 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 20: 46 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 47:57 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 58:86 )
9X-RAY DIFFRACTION9CHAIN D AND (RESID 21:33 )
10X-RAY DIFFRACTION10CHAIN D AND (RESID 34:45 )
11X-RAY DIFFRACTION11CHAIN A AND (RESID 65:86 )
12X-RAY DIFFRACTION12CHAIN A AND (RESID 87:115 )
13X-RAY DIFFRACTION13CHAIN A AND (RESID 116:135 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 94:115 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 116:131 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 87:125 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 126:135 )
18X-RAY DIFFRACTION18CHAIN D AND (RESID 46:78 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 79:116 )
20X-RAY DIFFRACTION20CHAIN D AND (RESID 117:142 )

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