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- PDB-6q36: TEAD4(216-434) complexed with optimized peptide 9 and myristoate ... -

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Basic information

Entry
Database: PDB / ID: 6q36
TitleTEAD4(216-434) complexed with optimized peptide 9 and myristoate (covalently bound) at 2.01A resolution: Structure-based design of potent linear peptide inhibitors of the YAP-TEAD protein-protein interaction derived from the YAP omega-loop sequence
Components
  • ACE-PRO-6CW-ARG-LEU-ARG-LYS-2JH-HYP-ASP-SER-PHE-ALN-LYS-GLU-PRO-NH2
  • Transcriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION / transcription factor / co-activator / transcription regulation
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) / 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 ...Transcriptional enhancer factor TEF-3 (TEAD4) / 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 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / PHOSPHATE ION / Transcriptional enhancer factor TEF-3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsKallen, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Structure-based design of potent linear peptide inhibitors of the YAP-TEAD protein-protein interaction derived from the YAP omega-loop sequence.
Authors: Furet, P. / Salem, B. / Mesrouze, Y. / Schmelzle, T. / Lewis, I. / Kallen, J. / Chene, P.
History
DepositionDec 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
B: Transcriptional enhancer factor TEF-3
C: ACE-PRO-6CW-ARG-LEU-ARG-LYS-2JH-HYP-ASP-SER-PHE-ALN-LYS-GLU-PRO-NH2
D: ACE-PRO-6CW-ARG-LEU-ARG-LYS-2JH-HYP-ASP-SER-PHE-ALN-LYS-GLU-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,14610
Polymers55,3094
Non-polymers8376
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.868, 40.438, 98.034
Angle α, β, γ (deg.)90.000, 93.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-675-

HOH

21A-716-

HOH

31B-705-

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: 25597.838 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 (bacteria) / References: UniProt: Q15561
#2: Protein/peptide ACE-PRO-6CW-ARG-LEU-ARG-LYS-2JH-HYP-ASP-SER-PHE-ALN-LYS-GLU-PRO-NH2


Mass: 2056.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.9 M NaK Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2013
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.01→19.8 Å / Num. obs: 45287 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 44.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.067 / Net I/σ(I): 12.1
Reflection shellResolution: 2.01→2.062 Å / Redundancy: 3 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.755 / Rrim(I) all: 0.65 / % possible all: 94.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q2X

6q2x


Resolution: 2.01→19.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.331 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1766 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.156
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 2265 5 %RANDOM
Rwork0.2166 ---
obs0.2179 43018 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.99 Å2 / Biso mean: 40.656 Å2 / Biso min: 21.49 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.08 Å2
2--0.06 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.01→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 0 344 243 4110
Biso mean--43.99 47.53 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214039
X-RAY DIFFRACTIONr_angle_refined_deg1.122.0335478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51824.286189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54915640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9621516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213110
LS refinement shellResolution: 2.01→2.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 157 -
Rwork0.398 2977 -
all-3134 -
obs--94.74 %

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