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- PDB-6gec: TEAD4 (216-434) COMPLEXED WITH YAP PEPTIDE (60-100);S94A AND MYRI... -

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Basic information

Entry
Database: PDB / ID: 6gec
TitleTEAD4 (216-434) COMPLEXED WITH YAP PEPTIDE (60-100);S94A AND MYRISTOATE (COVALENTLY BOUND) AT 1.70A (P41212 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA
Components
  • Transcriptional coactivator YAP1
  • Transcriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION / CO-ACTIVATOR COMPLEX / PROTEIN-PROTEIN INTERACTION
Function / homology
Function and homology information


trophectodermal cell fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / bud elongation involved in lung branching / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / glandular epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription ...trophectodermal cell fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / bud elongation involved in lung branching / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / glandular epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / heart process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of stem cell proliferation / tissue homeostasis / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / female germ cell nucleus / embryonic heart tube morphogenesis / proline-rich region binding / Signaling by Hippo / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / cell fate specification / organ growth / negative regulation of epithelial cell differentiation / muscle organ development / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / positive regulation of stem cell population maintenance / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / embryonic organ development / vasculogenesis / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / positive regulation of cardiac muscle cell proliferation / Nuclear signaling by ERBB4 / cellular response to retinoic acid / keratinocyte differentiation / extrinsic apoptotic signaling pathway / embryo implantation / positive regulation of epithelial cell proliferation / epithelial cell proliferation / skeletal system development / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / positive regulation of canonical Wnt signaling pathway / cell-cell junction / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / DNA-templated transcription / DNA damage response / chromatin binding / positive regulation of gene expression / chromatin / 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
Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A - #10 / Transcriptional enhancer factor TEF-3 (TEAD4) / Coagulation Factor XIII; Chain A, domain 1 - #80 / : / Omega loop, TEAD interating region 3 / : / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily ...Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A - #10 / Transcriptional enhancer factor TEF-3 (TEAD4) / Coagulation Factor XIII; Chain A, domain 1 - #80 / : / Omega loop, TEAD interating region 3 / : / 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 / Coagulation Factor XIII; Chain A, domain 1 / Other non-globular / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Distorted Sandwich / Special / Mainly Beta
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 / molecular replacement / Resolution: 1.7 Å
AuthorsKallen, J.
CitationJournal: Protein Sci. / Year: 2018
Title: Adaptation of the bound intrinsically disordered protein YAP to mutations at the YAP:TEAD interface.
Authors: Mesrouze, Y. / Bokhovchuk, F. / Izaac, A. / Meyerhofer, M. / Zimmermann, C. / Fontana, P. / Schmelzle, T. / Erdmann, D. / Furet, P. / Kallen, J. / Chene, P.
History
DepositionApr 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all ..._reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-3
L: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2603
Polymers30,0322
Non-polymers2281
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-16 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.882, 58.882, 158.508
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

21A-746-

HOH

31L-117-

HOH

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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.: 1 / 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 / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q15561
#2: Protein/peptide Transcriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 4531.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: S94A mutant / Source: (synth.) Homo sapiens (human) / References: UniProt: P46937
#3: Chemical ChemComp-MYR / MYRISTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M NaTartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2018
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 1.7→19.81 Å / Num. obs: 31611 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.083 / Net I/σ(I): 21.8 / Num. measured all: 405950
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 3.3 / CC1/2: 0.919 / Rrim(I) all: 1.051 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GE3

6ge3


Resolution: 1.7→19.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.312 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.116
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 1581 5 %RANDOM
Rwork0.2199 ---
obs0.2209 30030 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.03 Å2 / Biso mean: 24.409 Å2 / Biso min: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.7→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 15 205 2242
Biso mean--34.26 33.69 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222149
X-RAY DIFFRACTIONr_angle_refined_deg0.961.9552917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3795265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46224.057106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78815374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5241511
X-RAY DIFFRACTIONr_chiral_restr0.0630.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211644
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 115 -
Rwork0.289 2178 -
all-2293 -
obs--99.96 %

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