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- PDB-8a0u: Crystal structure of TEAD3 in complex with CPD4 -

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Basic information

Entry
Database: PDB / ID: 8a0u
TitleCrystal structure of TEAD3 in complex with CPD4
ComponentsTranscriptional enhancer factor TEF-5
KeywordsTRANSCRIPTION / Inhibitor / Complex
Function / homology
Function and homology information


RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / asymmetric neuroblast division / hippo signaling / positive regulation of stem cell population maintenance / embryonic organ development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / asymmetric neuroblast division / hippo signaling / positive regulation of stem cell population maintenance / embryonic organ development / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Transcriptional enhancer factor TEF-5 (TEAD3) / 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
Chem-KMU / MYRISTIC ACID / PHOSPHATE ION / Transcriptional enhancer factor TEF-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.895 Å
AuthorsScheufler, C. / Kallen, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemmedchem / Year: 2022
Title: The First Class of Small Molecules Potently Disrupting the YAP-TEAD Interaction by Direct Competition.
Authors: Furet, P. / Bordas, V. / Le Douget, M. / Salem, B. / Mesrouze, Y. / Imbach-Weese, P. / Sellner, H. / Voegtle, M. / Soldermann, N. / Chapeau, E. / Wartmann, M. / Scheufler, C. / Fernandez, C. ...Authors: Furet, P. / Bordas, V. / Le Douget, M. / Salem, B. / Mesrouze, Y. / Imbach-Weese, P. / Sellner, H. / Voegtle, M. / Soldermann, N. / Chapeau, E. / Wartmann, M. / Scheufler, C. / Fernandez, C. / Kallen, J. / Guagnano, V. / Chene, P. / Schmelzle, T.
History
DepositionMay 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 19, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-5
B: Transcriptional enhancer factor TEF-5
C: Transcriptional enhancer factor TEF-5
D: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,52420
Polymers101,3354
Non-polymers3,18916
Water4,071226
1
A: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2266
Polymers25,3341
Non-polymers8925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9413
Polymers25,3341
Non-polymers6072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2266
Polymers25,3341
Non-polymers8925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1315
Polymers25,3341
Non-polymers7974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.265, 128.607, 156.107
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-5 / DTEF-1 / ETF-related factor 1 / ETFR-1 / TEA domain family member 3 / TEAD-3


Mass: 25333.842 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Tead3, Tcf13r2, Tef5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P70210
#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical
ChemComp-KMU / 2-[(2~{S})-2-(aminomethyl)-5-chloranyl-2-phenyl-3~{H}-1-benzofuran-4-yl]benzamide


Mass: 378.851 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H19ClN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.1 - 1.4 M sodium/potassium phosphate pH 5.6

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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 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.895→24.638 Å / Num. obs: 27738 / % possible obs: 92.2 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.158 / Net I/σ(I): 10.5
Reflection shellResolution: 2.895→2.98 Å / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1388 / CC1/2: 0.823

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (3-FEB-2022)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Previous in-house structure

Resolution: 2.895→24.64 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.852 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.401
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1383 -RANDOM
Rwork0.2116 ---
obs0.2144 27738 92.5 %-
Displacement parametersBiso mean: 34.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.1696 Å20 Å20 Å2
2---3.6384 Å20 Å2
3----0.5312 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.895→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 148 226 7080
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087058HARMONIC2
X-RAY DIFFRACTIONt_angle_deg19541HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2423SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1162HARMONIC5
X-RAY DIFFRACTIONt_it7058HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion883SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5091SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion17.96
LS refinement shellResolution: 2.9→2.93 Å
RfactorNum. reflection% reflection
Rfree0.3703 28 -
Rwork0.2635 --
obs0.2689 555 50.6 %

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