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- PDB-7typ: TEAD2 bound to GNE-7883 -

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Basic information

Entry
Database: PDB / ID: 7typ
TitleTEAD2 bound to GNE-7883
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / Small molecule PPI inhibitor complex
Function / homology
Function and homology information


TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / notochord development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / paraxial mesoderm development / hippo signaling / regulation of stem cell differentiation / Formation of axial mesoderm / embryonic heart tube morphogenesis ...TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / notochord development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / paraxial mesoderm development / hippo signaling / regulation of stem cell differentiation / Formation of axial mesoderm / embryonic heart tube morphogenesis / vasculogenesis / embryonic organ development / cellular response to retinoic acid / neural tube closure / transcription coactivator binding / sequence-specific double-stranded DNA binding / disordered domain specific binding / protein-containing complex assembly / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Chem-KUR / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNoland, C.L. / Fong, R.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Novel mechanism of YAP-TEAD inhibition results in targeted chromatin remodeling and reveals an expanded Hippo dependent landscape in cancers
Authors: Hagenbeek, T.J. / Zbieg, J.R. / Noland, C.L. / Yao, X. / Schmidt, S. / Clausen, S. / Steffek, M. / Lee, W. / Beroza, P. / Martin, S. / Lin, E. / Fong, R. / Di Lello, P. / Kubala, M.H. / ...Authors: Hagenbeek, T.J. / Zbieg, J.R. / Noland, C.L. / Yao, X. / Schmidt, S. / Clausen, S. / Steffek, M. / Lee, W. / Beroza, P. / Martin, S. / Lin, E. / Fong, R. / Di Lello, P. / Kubala, M.H. / Lacap, J.A. / Yang, M.N.Y. / Maddalo, D. / Lau, J.T. / An, L. / Levy, E. / Lorenzo, M.N. / Lee, H.J. / Pham, T.H. / Modrusan, Z. / Zang, R. / Chen, Y.C. / Li, J. / Hafner, M. / Chang, M.T. / Crawford, J.J. / Dey, A.
History
DepositionFeb 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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-4
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7255
Polymers52,6022
Non-polymers1,1233
Water3,405189
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9233
Polymers26,3011
Non-polymers6232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8012
Polymers26,3011
Non-polymers5011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.970, 61.430, 80.052
Angle α, β, γ (deg.)90.000, 117.178, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Transcriptional enhancer factor TEF-4 / TEA domain family member 2 / TEAD-2


Mass: 26300.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD2, TEF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15562
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-KUR / (8S)-5-(4-cyclohexylphenyl)-3-[3-(fluoromethyl)azetidine-1-carbonyl]-2-(3-methylpyrazin-2-yl)pyrazolo[1,5-a]pyrimidin-7(4H)-one


Mass: 500.567 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H29FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Na/K Tartrate, 0.1 M Bis Tris pH 6.5, 35% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.597→71.21 Å / Num. obs: 42783 / % possible obs: 60.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.63 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.2
Reflection shellResolution: 1.597→1.763 Å / Num. unique obs: 7572 / CC1/2: 0.652

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMV

5emv


Resolution: 1.6→71.21 Å / SU ML: 0.1729 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0601
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2156 2117 4.95 %
Rwork0.184 40665 -
obs0.1855 42782 60.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→71.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 82 189 3509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983564
X-RAY DIFFRACTIONf_angle_d1.13154876
X-RAY DIFFRACTIONf_chiral_restr0.0697534
X-RAY DIFFRACTIONf_plane_restr0.0068666
X-RAY DIFFRACTIONf_dihedral_angle_d21.5121367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.50320.327468X-RAY DIFFRACTION1.5
1.63-1.670.324210.2958302X-RAY DIFFRACTION6.94
1.67-1.720.2405370.2723677X-RAY DIFFRACTION15.3
1.72-1.770.3148670.27781201X-RAY DIFFRACTION27.07
1.77-1.830.25961010.26641691X-RAY DIFFRACTION38.45
1.83-1.890.24251190.24842261X-RAY DIFFRACTION51.04
1.89-1.970.2429950.22221966X-RAY DIFFRACTION43.77
1.97-2.060.25571870.21443334X-RAY DIFFRACTION75.24
2.06-2.170.24131930.21053420X-RAY DIFFRACTION77.2
2.17-2.30.22012030.20683940X-RAY DIFFRACTION87.96
2.3-2.480.24062210.20434420X-RAY DIFFRACTION98.87
2.48-2.730.26862160.20634265X-RAY DIFFRACTION94.84
2.73-3.130.24782210.19454441X-RAY DIFFRACTION98.46
3.13-3.940.16341940.15684139X-RAY DIFFRACTION91.76
3.94-71.210.1922400.15834540X-RAY DIFFRACTION98.6

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