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- PDB-6hik: X-ray structure of TEAD4(Y429H) mutant) complexed with YAP (wildt... -

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Basic information

Entry
Database: PDB / ID: 6hik
TitleX-ray structure of TEAD4(Y429H) mutant) complexed with YAP (wildtype): Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy
Components
  • Transcriptional coactivator YAP1
  • Transcriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of stem cell proliferation / cardiac muscle tissue regeneration / polarized epithelial cell differentiation / TEAD-YAP complex / negative regulation of epithelial cell apoptotic process / RUNX3 regulates YAP1-mediated transcription / organ growth / negative regulation of cilium assembly / tissue homeostasis / epithelial cell proliferation ...regulation of stem cell proliferation / cardiac muscle tissue regeneration / polarized epithelial cell differentiation / TEAD-YAP complex / negative regulation of epithelial cell apoptotic process / RUNX3 regulates YAP1-mediated transcription / organ growth / negative regulation of cilium assembly / tissue homeostasis / epithelial cell proliferation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / intestinal epithelial cell development / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Formation of axial mesoderm / heart process / Signaling by Hippo / proline-rich region binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / negative regulation of fat cell differentiation / embryonic organ development / muscle organ development / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / positive regulation of cardiac muscle cell proliferation / positive regulation of osteoblast differentiation / response to progesterone / skeletal system development / regulation of neurogenesis / bicellular tight junction / Nuclear signaling by ERBB4 / positive regulation of epithelial cell proliferation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / wound healing / Developmental Lineage of Pancreatic Ductal Cells / cellular response to gamma radiation / positive regulation of protein localization to nucleus / protein-DNA complex / transcription coregulator activity / cell-cell junction / transcription corepressor activity / Regulation of PD-L1(CD274) transcription / positive regulation of cell growth / transcription regulator complex / RUNX1 regulates transcription of genes involved in differentiation of HSCs / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / positive regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / DNA damage response / nucleolus / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A - #10 / Transcriptional enhancer factor TEF-3 (TEAD4) / : / Omega loop, TEAD interacting region 3 / : / Coagulation Factor XIII; Chain A, domain 1 - #80 / 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) / : / Omega loop, TEAD interacting region 3 / : / Coagulation Factor XIII; Chain A, domain 1 - #80 / 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 / Special / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / PHOSPHATE ION / Transcriptional coactivator YAP1 / Transcriptional enhancer factor TEF-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsKallen, J.
CitationJournal: Febs J. / Year: 2019
Title: Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy.
Authors: Bokhovchuk, F. / Mesrouze, Y. / Izaac, A. / Meyerhofer, M. / Zimmermann, C. / Fontana, P. / Schmelzle, T. / Erdmann, D. / Furet, P. / Kallen, J. / Chene, P.
History
DepositionAug 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 9, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all
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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)30,4415
Polymers30,0232
Non-polymers4183
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-29 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.843, 58.843, 159.101
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-746-

HOH

21L-139-

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: 25475.693 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(DE3) (bacteria) / References: UniProt: Q15561
#2: Protein/peptide Transcriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 4547.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 46.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.4M Na/K PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99981 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2018
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99981 Å / Relative weight: 1
ReflectionResolution: 1.65→19.95 Å / Num. obs: 34599 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.083 / Net I/σ(I): 21 / Num. measured all: 449159
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.6 / Rpim(I) all: 0.88 / Rrim(I) all: 1.05 / % 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: 1.65→19.95 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.037 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.107
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 1730 5 %RANDOM
Rwork0.2245 ---
obs0.2252 32868 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 52.58 Å2 / Biso mean: 23.128 Å2 / Biso min: 11.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.65→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 25 203 2307
Biso mean--32.97 32.18 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222248
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.963067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1735284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37724.128109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63915390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6321511
X-RAY DIFFRACTIONr_chiral_restr0.0690.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211722
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 125 -
Rwork0.303 2377 -
all-2502 -
obs--100 %

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