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- PDB-8c17: Crystal structure of TEAD4 in complex with peptide 1 -

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Basic information

Entry
Database: PDB / ID: 8c17
TitleCrystal structure of TEAD4 in complex with peptide 1
Components
  • Stapled peptide
  • Transcriptional 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
MYRISTIC ACID / Transcriptional enhancer factor TEF-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsScheufler, C. / Kallen, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Biochemical and Structural Characterization of a Peptidic Inhibitor of the YAP:TEAD Interaction That Binds to the alpha-Helix Pocket on TEAD.
Authors: Mesrouze, Y. / Gubler, H. / Villard, F. / Boesch, R. / Ottl, J. / Kallen, J. / Reid, P.C. / Scheufler, C. / Marzinzik, A.L. / Chene, P.
History
DepositionDec 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 29, 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: Stapled peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2615
Polymers27,8482
Non-polymers4133
Water1,02757
1
A: Transcriptional enhancer factor TEF-3
B: Stapled peptide
hetero molecules

A: Transcriptional enhancer factor TEF-3
B: Stapled peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,52210
Polymers55,6974
Non-polymers8256
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3690 Å2
ΔGint12 kcal/mol
Surface area11300 Å2
Unit cell
Length a, b, c (Å)54.468, 54.468, 166.429
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD4, RTEF1, TCF13L1, TEF3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q15561
#2: Protein/peptide Stapled peptide


Mass: 2250.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4 M sodium malonate

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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 EIGER2 X 16M / Detector: PIXEL / Date: Sep 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→24.45 Å / Num. obs: 12749 / % possible obs: 89.4 % / Redundancy: 15 % / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Net I/σ(I): 12
Reflection shellResolution: 2.25→2.34 Å / Rmerge(I) obs: 1.332 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 639 / CC1/2: 0.819

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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: 2.25→18.49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.314 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.33 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.219
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 612 -RANDOM
Rwork0.2092 ---
obs0.2106 12728 89.3 %-
Displacement parametersBiso mean: 47.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.9101 Å20 Å20 Å2
2--0.9101 Å20 Å2
3----1.8202 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.25→18.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 168 57 1986
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081984HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.992688HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d674SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes333HARMONIC5
X-RAY DIFFRACTIONt_it1984HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion247SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1418SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion11.22
LS refinement shellResolution: 2.25→2.31 Å
RfactorNum. reflection% reflection
Rfree0.1993 20 -
Rwork0.2357 --
obs0.2339 425 39.27 %
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)
10.80260.7170.80581.37240.9611.5819-0.0938-0.0872-0.1775-0.08720.0876-0.0114-0.1775-0.01140.00610.0080.02680.0108-0.06480.0006-0.0832-25.787511.172-14.2607
213.51462.38934.13011.22244.431615.4934-0.4508-0.4334-0.6335-0.43340.15840.077-0.63350.0770.29240.1391-0.14090.0281-0.19890.056-0.1549-15.866429.9963-15.7044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A215 - 502
2X-RAY DIFFRACTION2{ B|* }B1 - 19

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