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- PDB-2ce9: A WRPW peptide bound to the Groucho-TLE WD40 domain. -

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Basic information

Entry
Database: PDB / ID: 2ce9
TitleA WRPW peptide bound to the Groucho-TLE WD40 domain.
Components
  • TRANSDUCIN-LIKE ENHANCER PROTEIN 1
  • WRPW PEPTIDE
KeywordsTRANSCRIPTION REGULATION / TRANSCRIPTIONAL CO-REPRESSOR / WD40 DOMAIN / WNT SIGNALING PATHWAY / NUCLEAR PROTEIN / PHOSPHORYLATION / REPRESSOR / TRANSCRIPTION / WD REPEAT
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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...Groucho/TLE, N-terminal Q-rich domain / Groucho/TLE N-terminal Q-rich domain / Groucho/transducin-like enhancer / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Mainly Beta
Similarity search - Domain/homology
Transducin-like enhancer protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsPickles, L.M. / Roe, S.M. / Pearl, L.H.
Citation
Journal: Mol.Cell / Year: 2006
Title: Molecular Recognition of Transcriptional Repressor Motifs by the Wd Domain of the Groucho/Tle Corepressor.
Authors: Jennings, B.H. / Pickles, L.M. / Wainwright, S.M. / Roe, S.M. / Pearl, L.H. / Ish-Horowicz, D.
#1: Journal: Structure / Year: 2002
Title: Crystal Structure of the C-Terminal Wd40 Repeat Domain of the Human Groucho-Tle1 Transcriptional Corepressor.
Authors: Pickles, L.M. / Roe, S.M. / Hemingway, E.J. / Stifani, S. / Pearl, L.H.
History
DepositionFeb 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.4Dec 13, 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: TRANSDUCIN-LIKE ENHANCER PROTEIN 1
B: TRANSDUCIN-LIKE ENHANCER PROTEIN 1
C: TRANSDUCIN-LIKE ENHANCER PROTEIN 1
D: TRANSDUCIN-LIKE ENHANCER PROTEIN 1
X: WRPW PEPTIDE
Y: WRPW PEPTIDE


Theoretical massNumber of molelcules
Total (without water)148,9666
Polymers148,9666
Non-polymers00
Water15,511861
1
A: TRANSDUCIN-LIKE ENHANCER PROTEIN 1
B: TRANSDUCIN-LIKE ENHANCER PROTEIN 1
X: WRPW PEPTIDE


Theoretical massNumber of molelcules
Total (without water)74,4833
Polymers74,4833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: TRANSDUCIN-LIKE ENHANCER PROTEIN 1
D: TRANSDUCIN-LIKE ENHANCER PROTEIN 1
Y: WRPW PEPTIDE


Theoretical massNumber of molelcules
Total (without water)74,4833
Polymers74,4833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)107.810, 56.478, 126.642
Angle α, β, γ (deg.)90.00, 112.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TRANSDUCIN-LIKE ENHANCER PROTEIN 1 / ESG1 / E(SP1) HOMOLOG


Mass: 36853.469 Da / Num. of mol.: 4
Fragment: PARTIAL SP AND WHOLE WD40 DOMAINS, RESIDUES 443-770
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q04724
#2: Protein/peptide WRPW PEPTIDE


Mass: 775.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRANSCRIPTIONAL COREPRESSOR THAT BINDS TO A NUMBER OF TRANSCRIPTION FACTORS

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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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 287 K / Method: microbatch / pH: 6.5
Details: 6MG/ML PROTEIN WAS MIXED 1:1 WITH 12% PEG8000, 100MM NACACODYLATE PH6.5, 100MM NAACETATE AT 14C IN MICROBATCH. PEPTIDES WERE ADDED TO THE PROTEIN CRYSTALS IN 125 MM NACL, 25 MM TRIS PH8.0, 0. ...Details: 6MG/ML PROTEIN WAS MIXED 1:1 WITH 12% PEG8000, 100MM NACACODYLATE PH6.5, 100MM NAACETATE AT 14C IN MICROBATCH. PEPTIDES WERE ADDED TO THE PROTEIN CRYSTALS IN 125 MM NACL, 25 MM TRIS PH8.0, 0.5 MM EDTA TO A FINAL CONCENTRATION OF 0.76 MM, AND INCUBATED FOR 16 H BEFORE HARVESTING AND WASHING IN 50MM NA CACODYLATE PH6.5, 12 % PEG 8K, AND CRYO-PROTECTED IN 30% ETHYLENE GLYCOL 50MM NA CACODYLATE PH6.5, 12 % PEG 8K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.12→45 Å / Num. obs: 78005 / % possible obs: 97.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 2.12→2.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.6 / % possible all: 83

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GXR

1gxr


Resolution: 2.12→117.04 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.309 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3924 5 %RANDOM
Rwork0.178 ---
obs0.181 74067 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-0.65 Å2
2--0.15 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.12→117.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10424 0 0 861 11285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02210695
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.9414568
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.63651346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09224.298456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.151151684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0191546
X-RAY DIFFRACTIONr_chiral_restr0.1350.21601
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028186
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.24734
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.27003
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2942
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1371.56921
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.845210870
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.67734430
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8574.53698
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
LS refinement shellResolution: 2.12→2.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.33 203
Rwork0.207 3870
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)
10.80740.09730.00490.5634-0.07910.7164-0.02040.04190.0475-0.06870.03450.04280.0011-0.0093-0.0141-0.01750.0041-0.0006-0.0808-0.0046-0.0176-18.49281.402645.3339
21.1497-0.20510.25040.69060.0260.7813-0.0167-0.09230.06060.042-0.019-0.05670.01940.02830.0357-0.0415-0.01370.004-0.0614-0.0111-0.020725.0453-1.041471.9064
30.91930.0210.05370.57110.00420.9508-0.04560.00250.0598-0.08380.04870.0444-0.01330-0.0031-0.0187-0.0104-0.016-0.0851-0.0055-0.0235.94241.1736-12.9691
41.6249-0.14511.02340.9113-0.03811.8756-0.0135-0.07340.14120.0002-0.0705-0.09880.05970.07510.084-0.0484-0.0138-0.001-0.0741-0.0071-0.027649.7672-2.107513.4823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A434 - 770
2X-RAY DIFFRACTION1X2 - 6
3X-RAY DIFFRACTION2B434 - 770
4X-RAY DIFFRACTION3C434 - 770
5X-RAY DIFFRACTION3Y2 - 6
6X-RAY DIFFRACTION4D434 - 770

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