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- PDB-7tyu: TEAD2 bound to Compound 2 -

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Basic information

Entry
Database: PDB / ID: 7tyu
TitleTEAD2 bound to Compound 2
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-KTF / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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

Downloads & links

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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)53,5555
Polymers52,6022
Non-polymers9533
Water1,54986
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8383
Polymers26,3011
Non-polymers5382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7162
Polymers26,3011
Non-polymers4151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.270, 61.526, 79.412
Angle α, β, γ (deg.)90.000, 111.759, 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-KTF / (3R)-1-[(8S)-5-(4-cyclohexylphenyl)-7-oxo-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonyl]pyrrolidine-3-carbonitrile


Mass: 415.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
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: 1.78→53.835 Å / Num. obs: 31238 / % possible obs: 92.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.55 Å2 / CC1/2: 1 / Net I/σ(I): 14
Reflection shellResolution: 1.784→1.986 Å / Num. unique obs: 1536 / CC1/2: 0.783

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Processing

Software
NameVersionClassification
PHENIX1.18rc5_3822refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMV

5emv


Resolution: 1.78→33.35 Å / SU ML: 0.229 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.5516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2302 1561 5 %
Rwork0.1969 29672 -
obs0.1986 31233 62.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.7 Å2
Refinement stepCycle: LAST / Resolution: 1.78→33.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 70 86 3369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313433
X-RAY DIFFRACTIONf_angle_d0.69414667
X-RAY DIFFRACTIONf_chiral_restr0.0438504
X-RAY DIFFRACTIONf_plane_restr0.0037631
X-RAY DIFFRACTIONf_dihedral_angle_d22.61681292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.840.512160.435390X-RAY DIFFRACTION2.14
1.84-1.90.2965180.335340X-RAY DIFFRACTION8.18
1.9-1.980.3547590.2658912X-RAY DIFFRACTION21.24
1.98-2.070.2645860.27421703X-RAY DIFFRACTION40.16
2.07-2.180.28251420.26892563X-RAY DIFFRACTION59.94
2.18-2.310.26911640.25473193X-RAY DIFFRACTION74.83
2.31-2.490.28292130.26143890X-RAY DIFFRACTION90.85
2.49-2.740.28032140.26194253X-RAY DIFFRACTION98.37
2.74-3.140.27562090.23124233X-RAY DIFFRACTION98.01
3.14-3.950.25312050.17464231X-RAY DIFFRACTION97.84
3.95-33.350.16972450.15474264X-RAY DIFFRACTION96.88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3599957049810.466313182547-0.9432626783143.01529920548-0.3312931476012.744630333430.255178439783-0.852440153094-0.9490857883940.1920502235630.102090213783-0.2156954720940.859052306352-0.5737513367660.03949809069230.318837901147-0.0717033238285-0.04123579882320.3966301164550.04818796213040.264589014739-34.260790481-15.207536571325.099954399
20.1664104964070.08585739054850.1423738113960.4803265009220.2956685285660.474613162217-0.06923358226751.25722308354-0.00482792047628-1.544856476630.71575958265-0.766986124821-0.1457820297610.904479419220.01727398507820.76272229087-0.01019668936770.05694512477761.015728033720.04404888490040.606219128937-14.6392987525-8.6688668036312.1807216723
31.27870081418-1.24931093034-1.058569504761.591111982390.03545244078953.01340384772-0.2734750812070.06364085472510.255155856062-0.6207480293550.148416086889-0.427316752185-0.05673804576130.542480836935-0.00918725861440.282334366099-0.011789373755-0.05733412115870.223827496715-0.03590923941960.35210147472-22.0983172777-10.481722858917.9231661061
42.720475344590.03934217913251.570154298221.876655185360.6829776128241.19506060373-0.0881053149325-0.4627153504460.1021991498120.0831512215228-0.0234088754452-0.292310465945-0.240175557492-0.5234029018376.79779444554E-50.2758355678280.0425758165879-0.02104441498160.346007472195-0.04623344612010.281915753721-30.4985014594-4.0879157432427.8869119226
52.73173631373-0.09570731485930.09125781349032.275881725510.3297552412474.173394881410.07699031115960.193632512695-0.184763229007-0.209835551230.122950602081-0.1683243316670.341432920191-0.06431963154390.003691852332550.273127772740.007604778650650.01562236304270.120995369608-0.004494433749190.246926552031-27.9404645616-11.327513082913.9646538116
61.43043504772-0.112635145133-1.76645382722.71576889139-1.107647154013.107286068070.1725776619120.09713847625740.0958274137791-0.1846865458740.08977853006120.333417981281-0.04638722280410.03204824233681.47164271112E-50.3820271620820.04512050867410.007232251079730.416146715836-0.02659163356870.373606936374-35.934891424821.883768459620.9223405224
71.849747289020.697981044184-1.515024472022.34214073438-0.9775572305576.604624223530.0541903357945-0.3098356024080.18389350554-0.06877182123080.03737353560720.1271674906990.3220098610230.416558412987-0.007879511756550.238445368140.0855672771038-0.002673907306370.219811803160.002748725634720.300078046809-33.788308086718.062797635521.1204283452
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 220 through 266 )AA220 - 2661 - 47
22chain 'A' and (resid 267 through 284 )AA267 - 28448 - 65
33chain 'A' and (resid 285 through 325 )AA285 - 32566 - 91
44chain 'A' and (resid 326 through 380 )AA326 - 38092 - 151
55chain 'A' and (resid 381 through 446 )AA381 - 446152 - 220
66chain 'B' and (resid 222 through 284 )BD222 - 2841 - 47
77chain 'B' and (resid 285 through 446 )BD285 - 44648 - 197

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