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- PDB-7tyq: TEAD2 bound to Compound 1 -

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Basic information

Entry
Database: PDB / ID: 7tyq
TitleTEAD2 bound to Compound 1
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-KUI / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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)53,3044
Polymers52,6022
Non-polymers7032
Water1,20767
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6522
Polymers26,3011
Non-polymers3511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6522
Polymers26,3011
Non-polymers3511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.854, 61.183, 79.951
Angle α, β, γ (deg.)90.000, 111.608, 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-KUI / ethyl (8S)-7-oxo-5-[4-(trifluoromethyl)phenyl]-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carboxylate


Mass: 351.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
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: Jul 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.878→74.33 Å / Num. obs: 28082 / % possible obs: 94.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 34.9 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.2
Reflection shellResolution: 1.878→2.059 Å / Num. unique obs: 1405 / CC1/2: 0.711

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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: 1.88→74.33 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.7281
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2467 1415 5.04 %
Rwork0.206 26664 -
obs0.208 28079 66.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.99 Å2
Refinement stepCycle: LAST / Resolution: 1.88→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 50 67 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383393
X-RAY DIFFRACTIONf_angle_d0.66674618
X-RAY DIFFRACTIONf_chiral_restr0.0453504
X-RAY DIFFRACTIONf_plane_restr0.0032630
X-RAY DIFFRACTIONf_dihedral_angle_d22.08511257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.940.381160.306274X-RAY DIFFRACTION6.88
1.94-2.020.3967410.2783624X-RAY DIFFRACTION15.86
2.02-2.110.2808630.27071190X-RAY DIFFRACTION29.78
2.11-2.230.3022980.26011975X-RAY DIFFRACTION49.63
2.23-2.370.28861410.26722817X-RAY DIFFRACTION69.95
2.37-2.550.31992000.26913575X-RAY DIFFRACTION90.35
2.55-2.80.29372220.27084019X-RAY DIFFRACTION99.95
2.8-3.210.26912140.23434020X-RAY DIFFRACTION99.93
3.21-4.040.24992030.17924059X-RAY DIFFRACTION99.98
4.04-74.330.19352170.16854111X-RAY DIFFRACTION99.84
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)
12.26589134638-0.5393087613871.758165079162.284954899920.748552310315.02134202909-0.137859361628-0.0909835481605-0.158081662059-0.1998778984120.207914542977-0.445624762290.2492241458720.413821959331-3.98442053074E-60.256787086801-0.03791136940280.01071260330070.275574878961-0.03737804992020.283336363491-26.4295261638-11.899956246621.1433104716
23.081006485940.2268314308720.3409438060651.701188531610.8180540993385.02862455171-0.0561661617833-0.1984434796260.00548228117749-0.2046136881710.189201561994-0.1914009737020.0458075380001-0.1773616523310.00440129145110.2142950214770.027470320569-0.0101924271190.11474557205-0.007399386384270.215599968545-28.9952002637-8.8115610093219.7685449739
31.623838993940.302861029252-1.818123004012.50359296036-1.245646167992.339045719940.1585229313910.2207776138320.0308533540724-0.2440269497350.07850163724130.293131905359-0.32572017494-0.0388171166176-0.0001603932906260.3469884977830.0374394588877-0.02151976866060.420100803974-0.02955672296460.368154255928-36.365405345821.222512951520.9719600454
40.471028371748-1.02104381668-0.5252163824772.548387610560.08802872464563.606486939540.0912402927311-0.2437929771150.09044952146-0.154936514407-0.05808001218240.0830219908458-0.0188517465876-0.0104392709657-0.0002631496790450.2462749683470.01979798970060.03330357365840.2733004049060.01513341920180.331740429074-37.337149932718.945252094923.5278074151
52.642287726930.0683725482959-1.741006270590.8160110850050.01461512226721.206828837040.232033709409-0.5304352010640.25612456693-0.7849670779490.09588527593010.3066908269291.070120870620.698854910240.2711985375190.608810452650.229403724952-0.08702049208140.06451148672480.1188700529470.216094821741-34.8477335989.2995102397422.2000877481
61.174282672160.77761033797-0.03607199049110.819175415492-0.3843425084290.6415430347820.0958869179214-0.6377856473350.152465509575-0.124095450120.149720888461-0.1679993536720.04406017745091.498959481010.002955535808390.3879270991610.159785197338-0.01952663414850.6490609615740.03493762233340.371512452652-26.015620827316.732836483524.319856259
71.110425474870.1668427694540.5315108314990.402607035060.4685720729520.6380010261610.2606015487710.1287755397910.305638432963-0.279941083410.2397730277160.000554566737012-0.3895785454130.1656218861930.001463896768940.4227009681810.0552090253090.06691858995150.214423307241-0.01643716696430.287001490699-32.515668451918.565214117912.1423082693
81.88820238584-1.315151241550.8259762322442.196076052390.9391804678843.172044045450.1592948468260.00908787210070.59811827581-0.1113229580310.4177925419070.376069571155-0.239043264463-0.5060473329120.02168917587090.2446892399920.07758244196650.0395115349620.1756549739290.03868984057320.348124659117-38.463935012822.663494044320.3028659287
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 293 )AA220 - 2931 - 70
22chain 'A' and (resid 294 through 446 )AA294 - 44671 - 218
33chain 'B' and (resid 222 through 284 )BC222 - 2841 - 46
44chain 'B' and (resid 285 through 339 )BC285 - 33947 - 87
55chain 'B' and (resid 340 through 362 )BC340 - 36288 - 112
66chain 'B' and (resid 363 through 395 )BC363 - 395113 - 147
77chain 'B' and (resid 396 through 414 )BC396 - 414148 - 166
88chain 'B' and (resid 415 through 446 )BC415 - 446167 - 200

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