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- PDB-6sba: Crystal Structure of mTEAD with a VGL4 Tertiary Structure Mimetic -

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Basic information

Entry
Database: PDB / ID: 6sba
TitleCrystal Structure of mTEAD with a VGL4 Tertiary Structure Mimetic
Components
  • Transcriptional enhancer factor TEF-3
  • Vestigial like 4 (Drosophila), isoform CRA_a
KeywordsSIGNALING PROTEIN / Hippo pathway / protein-protein interaction / macrocyclic peptide / tertiary structure mimetic
Function / homology
Function and homology information


RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell fate commitment / negative regulation of cardiac muscle cell proliferation / hippo signaling / blastocyst formation / cell fate specification / positive regulation of stem cell population maintenance / negative regulation of Wnt signaling pathway / negative regulation of hippo signaling ...RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell fate commitment / negative regulation of cardiac muscle cell proliferation / hippo signaling / blastocyst formation / cell fate specification / positive regulation of stem cell population maintenance / negative regulation of Wnt signaling pathway / negative regulation of hippo signaling / cell fate commitment / embryonic organ development / embryo implantation / protein-DNA complex / negative regulation of cell growth / transcription coactivator binding / positive regulation of protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription cofactor vestigial-like protein 4 / Transcription cofactor vestigial-like protein 4 / TDU repeat / Short repeats in human TONDU, fly vestigial and other proteins. / Transcriptional enhancer factor TEF-3 (TEAD4) / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. ...Transcription cofactor vestigial-like protein 4 / Transcription cofactor vestigial-like protein 4 / TDU repeat / Short repeats in human TONDU, fly vestigial and other proteins. / Transcriptional enhancer factor TEF-3 (TEAD4) / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. / TEA domain / YAP binding domain / YAP binding domain
Similarity search - Domain/homology
ACETYL GROUP / Uncharacterized protein / Transcriptional enhancer factor TEF-3 / Transcription cofactor vestigial-like protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsAdihou, H. / Grossmann, T.N. / Waldmann, H. / Gasper, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council678623 Germany
CitationJournal: Nat Commun / Year: 2020
Title: A protein tertiary structure mimetic modulator of the Hippo signalling pathway.
Authors: Adihou, H. / Gopalakrishnan, R. / Forster, T. / Gueret, S.M. / Gasper, R. / Geschwindner, S. / Carrillo Garcia, C. / Karatas, H. / Pobbati, A.V. / Vazquez-Chantada, M. / Davey, P. / Wassvik, ...Authors: Adihou, H. / Gopalakrishnan, R. / Forster, T. / Gueret, S.M. / Gasper, R. / Geschwindner, S. / Carrillo Garcia, C. / Karatas, H. / Pobbati, A.V. / Vazquez-Chantada, M. / Davey, P. / Wassvik, C.M. / Pang, J.K.S. / Soh, B.S. / Hong, W. / Chiarparin, E. / Schade, D. / Plowright, A.T. / Valeur, E. / Lemurell, M. / Grossmann, T.N. / Waldmann, H.
History
DepositionJul 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-3
B: Vestigial like 4 (Drosophila), isoform CRA_a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7158
Polymers28,2102
Non-polymers5056
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-17 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.500, 65.110, 74.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional enhancer factor TEF-3 / ETF-related factor 2 / ETFR-2 / TEA domain family member 4 / TEAD-4 / TEF-1-related factor 1 / TEF- ...ETF-related factor 2 / ETFR-2 / TEA domain family member 4 / TEAD-4 / TEF-1-related factor 1 / TEF-1-related factor FR-19 / RTEF-1


Mass: 26006.520 Da / Num. of mol.: 1 / Fragment: YAP binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tead4, Tcf13r1, Tef3, Tefr1 / Plasmid: pOPIN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon+RIL / References: UniProt: Q62296
#2: Protein/peptide Vestigial like 4 (Drosophila), isoform CRA_a


Mass: 2203.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q3TQI9, UniProt: Q80V24*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES, 15% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.3→49.142 Å / Num. obs: 67179 / % possible obs: 97.9 % / Redundancy: 13.296 % / Biso Wilson estimate: 19.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.102 / Χ2: 0.979 / Net I/σ(I): 11.96 / Num. measured all: 893245 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.3313.0433.0570.8562647499648030.4093.17996.1
1.33-1.3713.8732.441.1565440489247170.522.53196.4
1.37-1.4113.8081.9481.4663588478146050.5992.02296.3
1.41-1.4513.6621.5071.9660907460544580.7111.56596.8
1.45-1.513.5061.1652.6858858448643580.8581.2197.1
1.5-1.5512.9550.7734.1654852435042340.9360.80497.3
1.55-1.6112.4750.5715.3751097419640960.9530.59597.6
1.61-1.6814.0330.4277.5755332402739430.9780.44397.9
1.68-1.7514.1090.3319.4553644388038020.9850.34398
1.75-1.8413.8740.22712.4451238374236930.9920.23698.7
1.84-1.9413.6960.15816.3747442352034640.9940.16598.4
1.94-2.0613.1870.12319.6843727335933160.9950.12898.7
2.06-2.211.9950.122.0537616316631360.9950.10599.1
2.2-2.3713.0340.08825.3238216295429320.9970.09199.3
2.37-2.613.620.08427.4336978273327150.9970.08799.3
2.6-2.9113.2360.07829.532666247724680.9960.08299.6
2.91-3.3612.6050.07430.8227743220822010.9960.07799.7
3.36-4.1111.4010.0730.7621502189218860.9960.07399.7
4.11-5.8112.8280.0733.1718998148114810.9970.072100
5.81-49.14212.3470.07332.34107548748710.9950.07699.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å42.95 Å
Translation1.9 Å42.95 Å

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Processing

Software
NameVersionClassification
XDS31-MAR-2018data reduction
XSCALE31-MAR-2018data scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nl0

4nl0


Resolution: 1.3→49.142 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.95
RfactorNum. reflection% reflection
Rfree0.1746 3359 5 %
Rwork0.1506 --
obs0.1518 67170 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.35 Å2 / Biso mean: 36.841 Å2 / Biso min: 14.72 Å2
Refinement stepCycle: final / Resolution: 1.3→49.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 72 134 2131
Biso mean--91.62 39.42 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0242136
X-RAY DIFFRACTIONf_angle_d2.0282893
X-RAY DIFFRACTIONf_chiral_restr0.125308
X-RAY DIFFRACTIONf_plane_restr0.012363
X-RAY DIFFRACTIONf_dihedral_angle_d15.037825
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.31850.41481350.3396256896
1.3185-1.33820.35041370.3057259396
1.3382-1.35910.3061360.2735258396
1.3591-1.38140.31011350.2699258296
1.3814-1.40520.2991380.2492259197
1.4052-1.43080.26671350.2368258197
1.4308-1.45830.23961330.2259262197
1.4583-1.48810.26671450.2101261597
1.4881-1.52050.23731290.1759260297
1.5205-1.55580.21061380.1526262197
1.5558-1.59470.19871410.146262998
1.5947-1.63790.18451380.1357262698
1.6379-1.68610.15721390.1249264198
1.6861-1.74050.16941410.13266598
1.7405-1.80270.15961390.1265265598
1.8027-1.87490.171420.1295267699
1.8749-1.96020.13691380.1252266899
1.9602-2.06350.171460.1252268399
2.0635-2.19280.15961430.1243269599
2.1928-2.36210.15261410.1285272799
2.3621-2.59980.1521470.1452272699
2.5998-2.9760.20361420.15422766100
2.976-3.74920.17861470.15462786100
3.7492-49.1420.14861540.15112911100

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