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- PDB-8caa: Crystal structure of TEAD4 in complex with YTP-13 -

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Basic information

Entry
Database: PDB / ID: 8caa
TitleCrystal structure of TEAD4 in complex with YTP-13
ComponentsTranscriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION / Complex / Inhibitor
Function / homology
Function and homology information


trophectodermal cell fate commitment / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / Formation of axial mesoderm / cell fate specification / muscle organ development / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / embryonic organ development ...trophectodermal cell fate commitment / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / Formation of axial mesoderm / cell fate specification / muscle organ development / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / embryonic organ development / embryo implantation / skeletal system development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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
PHOSPHATE ION / Chem-U3F / Chem-U3O / Transcriptional enhancer factor TEF-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsScheufler, C. / Kallen, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemmedchem / Year: 2023
Title: Optimization of a Class of Dihydrobenzofurane Analogs toward Orally Efficacious YAP-TEAD Protein-Protein Interaction Inhibitors.
Authors: Sellner, H. / Chapeau, E. / Furet, P. / Voegtle, M. / Salem, B. / Le Douget, M. / Bordas, V. / Groell, J.M. / Le Goff, A.L. / Rouzet, C. / Wietlisbach, T. / Zimmermann, T. / McKenna, J. / ...Authors: Sellner, H. / Chapeau, E. / Furet, P. / Voegtle, M. / Salem, B. / Le Douget, M. / Bordas, V. / Groell, J.M. / Le Goff, A.L. / Rouzet, C. / Wietlisbach, T. / Zimmermann, T. / McKenna, J. / Brocklehurst, C.E. / Chene, P. / Wartmann, M. / Scheufler, C. / Kallen, J. / Williams, G. / Harlfinger, S. / Traebert, M. / Dumotier, B.M. / Schmelzle, T. / Soldermann, N.
History
DepositionJan 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-3
B: Transcriptional enhancer factor TEF-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2717
Polymers51,1962
Non-polymers2,0755
Water2,990166
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-5 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.729, 89.397, 135.473
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional enhancer factor TEF-3 / TEA domain family member 4 / TEAD-4 / Transcription factor 13-like 1 / Transcription factor RTEF-1


Mass: 25597.838 Da / Num. of mol.: 2 / Fragment: C-terminal domain, YAP binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD4, RTEF1, TCF13L1, TEF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15561
#2: Chemical ChemComp-U3F / 4-[bis(fluoranyl)methoxy]-2-[(2~{S})-5-chloranyl-6-fluoranyl-2-[[(4-oxidanylcyclohexyl)amino]methyl]-2-phenyl-3~{H}-1-benzofuran-4-yl]-3-fluoranyl-benzamide


Mass: 578.982 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H27ClF4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-U3O / (2~{R})-2-[2-chloranyl-5-[2-chloranyl-4-(trifluoromethyl)phenoxy]phenyl]sulfanylpropanoic acid


Mass: 411.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11Cl2F3O3S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 3350 (w/v) , 0.25 M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→19.44 Å / Num. obs: 26699 / % possible obs: 88.2 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.151 / Net I/σ(I): 9.6
Reflection shellResolution: 2→2.09 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.323 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1335 / CC1/2: 0.584 / Rrim(I) all: 1.436 / % possible all: 35.7

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→19.44 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.253 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 1263 -RANDOM
Rwork0.2127 ---
obs0.2138 26699 88.2 %-
Displacement parametersBiso mean: 31.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.1825 Å20 Å20 Å2
2--1.5716 Å20 Å2
3----1.3892 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.999→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 135 166 3631
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083601HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014898HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1216SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes604HARMONIC5
X-RAY DIFFRACTIONt_it3601HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion445SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2811SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion15.41
LS refinement shellResolution: 2→2.05 Å
RfactorNum. reflection% reflection
Rfree0.3367 31 -
Rwork0.275 --
obs0.2786 534 24.99 %
Refinement TLS params.

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)
10.533-0.0904-0.37120.95940.4190.84080.0582-0.0101-0.0675-0.01010.00850.0052-0.06750.0052-0.0668-0.05810.0217-0.00740.007-0.0395-0.06097.58473.5402-34.8124
20.62470.0112-0.01170.6978-0.0260.59020.0339-0.04270.0396-0.0427-0.0540.00240.03960.00240.0201-0.0523-0.0129-0.0121-0.00440.0188-0.0378-6.82482.3298-2.1515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A217 - 433
2X-RAY DIFFRACTION2B217 - 434

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