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- PDB-8a8r: Crystal structure of TEAD4 in complex with YAP peptide -

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Basic information

Entry
Database: PDB / ID: 8a8r
TitleCrystal structure of TEAD4 in complex with YAP peptide
Components
  • Isoform 7 of Transcriptional coactivator YAP1
  • Transcriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION / Complex
Function / homology
Function and homology information


trophectodermal cell fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription ...trophectodermal cell fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / regulation of stem cell proliferation / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / Signaling by Hippo / proline-rich region binding / cell fate specification / muscle organ development / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / negative regulation of fat cell differentiation / positive regulation of Notch signaling pathway / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / progesterone receptor signaling pathway / somatic stem cell population maintenance / regulation of neurogenesis / canonical Wnt signaling pathway / vasculogenesis / embryonic organ development / positive regulation of osteoblast differentiation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / Nuclear signaling by ERBB4 / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / embryo implantation / response to progesterone / epithelial cell proliferation / skeletal system development / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / cell-cell junction / positive regulation of canonical Wnt signaling pathway / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / transcription coactivator activity / transcription cis-regulatory region 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 gene expression / DNA-templated transcription / DNA damage response / chromatin binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / cytosol / 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 ...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 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
MYRISTIC ACID / Transcriptional coactivator YAP1 / Transcriptional enhancer factor TEF-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 Å
AuthorsScheufler, C. / Kallen, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2023
Title: N-terminal beta-strand in YAP is critical for stronger binding to scalloped relative to TEAD transcription factor.
Authors: Fedir, B. / Yannick, M. / Marco, M. / Patrizia, F. / Catherine, Z. / Frederic, V. / Dirk, E. / Joerg, K. / Clemens, S. / Camilo, V.V. / Patrick, C.
History
DepositionJun 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 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-3
B: Transcriptional enhancer factor TEF-3
L: Isoform 7 of Transcriptional coactivator YAP1
M: Isoform 7 of Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9236
Polymers62,4674
Non-polymers4572
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-30 kcal/mol
Surface area22470 Å2
Unit cell
Length a, b, c (Å)43.026, 76.71, 164.622
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: 25500.721 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q15561
#2: Protein Isoform 7 of Transcriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 5732.570 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: amino acids 50-100 N-terminal acetylated C-terminal amidated
Source: (synth.) Homo sapiens (human) / References: UniProt: P46937
#3: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM sodium acetate trihydrate pH 4.6 50 mM magnesium acetate tetrahydrate 25% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.696→19.389 Å / Num. obs: 39525 / % possible obs: 64.5 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.029 / Rrim(I) all: 0.072 / Net I/σ(I): 13
Reflection shellResolution: 1.696→1.821 Å / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1977 / CC1/2: 0.862 / Rpim(I) all: 0.271 / Rrim(I) all: 0.694 / % possible all: 17.1

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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: 1.696→19.39 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.191 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.157
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 1979 -RANDOM
Rwork0.2229 ---
obs0.224 39525 64.4 %-
Displacement parametersBiso mean: 30.43 Å2
Baniso -1Baniso -2Baniso -3
1-5.4754 Å20 Å20 Å2
2--4.1401 Å20 Å2
3----9.6154 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.696→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 32 278 4247
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084087HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.955508HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1425SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes681HARMONIC5
X-RAY DIFFRACTIONt_it4087HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion512SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3307SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion16.34
LS refinement shellResolution: 1.7→1.75 Å
RfactorNum. reflection% reflection
Rfree0.2502 33 -
Rwork0.2554 --
obs0.2552 791 15.17 %
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)
10.1772-0.4786-0.28390.88330.50452.2515-0.01970.0104-0.05330.0104-0.041-0.0801-0.0533-0.08010.06080.01390.0044-0.00420.0729-0.057-0.1257-10.258-2.522230.0972
20.1976-0.33450.33190.5486-0.18062.4252-0.0734-0.0288-0.2682-0.02880.00130.0359-0.26820.03590.07210.0903-0.02-0.02550.05070.0261-0.1495-7.9645-1.4266-8.3773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* L|* }A217 - 434
2X-RAY DIFFRACTION1{ A|* L|* }L53 - 99
3X-RAY DIFFRACTION2{ B|* M|* }B216 - 433
4X-RAY DIFFRACTION2{ B|* M|* }M53 - 99

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