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- PDB-6hil: X-ray structure of TEAD1(Y421H mutant) complexed with YAP(wildtyp... -

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Basic information

Entry
Database: PDB / ID: 6hil
TitleX-ray structure of TEAD1(Y421H 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-1
KeywordsTRANSCRIPTION / OTHER / TRANSCRIPTION FACTOR
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 / YAP1- and WWTR1 (TAZ)-stimulated gene expression ...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 / 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 / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / positive regulation of osteoblast differentiation / embryonic organ development / regulation of neurogenesis / bicellular tight junction / epithelial cell proliferation / positive regulation of cardiac muscle cell proliferation / Nuclear signaling by ERBB4 / response to progesterone / positive regulation of epithelial cell proliferation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Regulation of PD-L1(CD274) transcription / Developmental Lineage of Pancreatic Ductal Cells / wound healing / transcription coregulator activity / cellular response to gamma radiation / positive regulation of protein localization to nucleus / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / cell-cell junction / transcription corepressor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / transcription regulator complex / 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 / DNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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. ...: / 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 / 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 / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / Transcriptional enhancer factor TEF-1 / Transcriptional coactivator YAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 1.2Mar 4, 2020Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-1
L: Transcriptional coactivator YAP1
D: Transcriptional enhancer factor TEF-1
O: Transcriptional coactivator YAP1
B: Transcriptional enhancer factor TEF-1
M: Transcriptional coactivator YAP1
C: Transcriptional enhancer factor TEF-1
N: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,41012
Polymers119,4968
Non-polymers9134
Water2,522140
1
A: Transcriptional enhancer factor TEF-1
L: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1023
Polymers29,8742
Non-polymers2281
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-14 kcal/mol
Surface area12650 Å2
MethodPISA
2
D: Transcriptional enhancer factor TEF-1
O: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1023
Polymers29,8742
Non-polymers2281
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-15 kcal/mol
Surface area12580 Å2
MethodPISA
3
B: Transcriptional enhancer factor TEF-1
M: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1023
Polymers29,8742
Non-polymers2281
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-13 kcal/mol
Surface area12630 Å2
MethodPISA
4
C: Transcriptional enhancer factor TEF-1
N: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1023
Polymers29,8742
Non-polymers2281
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-15 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.125, 46.544, 144.337
Angle α, β, γ (deg.)98.610, 90.850, 108.140
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Transcriptional enhancer factor TEF-1 / NTEF-1 / Protein GT-IIC / TEA domain family member 1 / TEAD-1 / Transcription factor 13 / TCF-13


Mass: 25223.740 Da / Num. of mol.: 4 / Fragment: C-terminal domain, YAP binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / References: UniProt: P28347
#2: Protein/peptide
Transcriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 4650.309 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46937
#3: Chemical
ChemComp-MYR / MYRISTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 22% (w/v) PEG3350, 0.2M Na Malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2018
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→19.9 Å / Num. obs: 41611 / % possible obs: 95.5 % / Redundancy: 1.8 % / Biso Wilson estimate: 51.3 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.0998 / Rrim(I) all: 0.065 / Net I/σ(I): 10.9 / Num. measured all: 74068
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.2 / Rpim(I) all: 0.702 / Rrim(I) all: 0.804 / % possible all: 95.4

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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: 3KYS

3kys


Resolution: 2.3→19.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.755 / SU ML: 0.25 / SU R Cruickshank DPI: 0.5941 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.594 / ESU R Free: 0.286
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 2081 5 %RANDOM
Rwork0.2425 ---
obs0.2437 39530 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.82 Å2 / Biso mean: 48.846 Å2 / Biso min: 19.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å2-2.6 Å2-0.05 Å2
2--2.06 Å20.3 Å2
3----3.09 Å2
Refinement stepCycle: final / Resolution: 2.3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7720 0 64 140 7924
Biso mean--42.96 43.23 -
Num. residues----951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228044
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.95710837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.695971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85724.124388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.909151458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9531544
X-RAY DIFFRACTIONr_chiral_restr0.0690.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216016
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 155 -
Rwork0.379 2949 -
all-3104 -
obs--95.57 %

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