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- PDB-8p0m: Crystal structure of TEAD3 in complex with IAG933 -

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Basic information

Entry
Database: PDB / ID: 8p0m
TitleCrystal structure of TEAD3 in complex with IAG933
Components(Transcriptional enhancer factor TEF- ...) x 2
KeywordsTRANSCRIPTION / Inhibitor / Complex
Function / homology
Function and homology information


asymmetric neuroblast division / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / embryonic organ development / female pregnancy / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...asymmetric neuroblast division / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / embryonic organ development / female pregnancy / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Transcriptional enhancer factor TEF-5 (TEAD3) / 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-1PG / MYRISTIC ACID / : / Transcriptional enhancer factor TEF-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.961 Å
AuthorsScheufler, C. / Villard, F. / Chau, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Cancer / Year: 2024
Title: Direct and selective pharmacological disruption of the YAP-TEAD interface by IAG933 inhibits Hippo-dependent and RAS-MAPK-altered cancers.
Authors: Chapeau, E.A. / Sansregret, L. / Galli, G.G. / Chene, P. / Wartmann, M. / Mourikis, T.P. / Jaaks, P. / Baltschukat, S. / Barbosa, I.A.M. / Bauer, D. / Brachmann, S.M. / Delaunay, C. / ...Authors: Chapeau, E.A. / Sansregret, L. / Galli, G.G. / Chene, P. / Wartmann, M. / Mourikis, T.P. / Jaaks, P. / Baltschukat, S. / Barbosa, I.A.M. / Bauer, D. / Brachmann, S.M. / Delaunay, C. / Estadieu, C. / Faris, J.E. / Furet, P. / Harlfinger, S. / Hueber, A. / Jimenez Nunez, E. / Kodack, D.P. / Mandon, E. / Martin, T. / Mesrouze, Y. / Romanet, V. / Scheufler, C. / Sellner, H. / Stamm, C. / Sterker, D. / Tordella, L. / Hofmann, F. / Soldermann, N. / Schmelzle, T.
History
DepositionMay 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-5
B: Transcriptional enhancer factor TEF-5
C: Transcriptional enhancer factor TEF-5
D: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24415
Polymers101,7544
Non-polymers3,49011
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint34 kcal/mol
Surface area36650 Å2
Unit cell
Length a, b, c (Å)65.503, 127.236, 155.536
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Transcriptional enhancer factor TEF- ... , 2 types, 4 molecules ABCD

#1: Protein Transcriptional enhancer factor TEF-5 / DTEF-1 / TEA domain family member 3 / TEAD-3


Mass: 25333.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD3, TEAD5, TEF5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q99594
#2: Protein Transcriptional enhancer factor TEF-5


Mass: 25543.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 5 types, 363 molecules

#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H24O6
#4: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#5: Chemical
ChemComp-WCF / 4-[(2~{S})-5-chloranyl-6-fluoranyl-2-phenyl-2-[(2~{S})-pyrrolidin-2-yl]-3~{H}-1-benzofuran-4-yl]-5-fluoranyl-6-(2-hydroxyethyloxy)-~{N}-methyl-pyridine-3-carboxamide


Mass: 529.963 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H26ClF2N3O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.18 Å3/Da / Density % sol: 61.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Hepes, Magnesium chloride hexahydrate, PEG monomethyl-ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.21421 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21421 Å / Relative weight: 1
ReflectionResolution: 1.96→98.48 Å / Num. obs: 78842 / % possible obs: 84 % / Redundancy: 25 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.133 / Net I/σ(I): 17.5
Reflection shellResolution: 1.961→2.034 Å / Rmerge(I) obs: 1.596 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3756 / CC1/2: 0.756 / Rrim(I) all: 1.645

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.961→98.48 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.171 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 3974 -RANDOM
Rwork0.2141 ---
obs0.215 78842 84 %-
Displacement parametersBiso mean: 37.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.9593 Å20 Å20 Å2
2--3.9553 Å20 Å2
3----2.996 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.961→98.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6670 0 237 352 7259
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087187HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.979699HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2510SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1182HARMONIC5
X-RAY DIFFRACTIONt_it7187HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion894SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5473SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion14.73
LS refinement shellResolution: 1.961→2 Å
RfactorNum. reflection% reflection
Rfree0.2858 70 -
Rwork0.2381 --
obs--32.92 %
Refinement TLS params.

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)
11.2447-0.0818-0.14630.4015-0.05370.9556-0.05130.02660.0150.02660.0638-0.11830.015-0.1183-0.0125-0.07410.02170.0340.0161-0.0122-0.0664-15.3184-8.117121.1051
20.7937-0.2186-0.17140.70880.14710.92930.0131-0.03510.0345-0.03510.02460.04780.03450.0478-0.0377-0.0704-0.00090.02090.0220.0301-0.066727.316-14.4762-27.0734
30.2067-0.0836-0.05890.76790.47841.8347-0.04530.0201-0.07230.0201-0.0010.1611-0.07230.16110.0463-0.09220.0025-0.00880.0419-0.0066-0.070711.20830.175913.6397
40.5714-0.0740.02340.697-0.23491.7736-0.0396-0.0101-0.0445-0.0101-0.0758-0.0243-0.0445-0.02430.1154-0.09930.0136-0.0150.03840.0061-0.07631.0176-3.8953-21.0698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* L|* }A218 - 434
2X-RAY DIFFRACTION1{ A|* L|* }A501 - 502
3X-RAY DIFFRACTION1{ A|* L|* }L1
4X-RAY DIFFRACTION2{ B|* M|* }B218 - 435
5X-RAY DIFFRACTION2{ B|* M|* }B501 - 502
6X-RAY DIFFRACTION2{ B|* M|* }M1
7X-RAY DIFFRACTION3{ C|* N|* }C218 - 435
8X-RAY DIFFRACTION3{ C|* N|* }C501
9X-RAY DIFFRACTION3{ C|* N|* }N1
10X-RAY DIFFRACTION4{ D|* O|* }D219 - 435
11X-RAY DIFFRACTION4{ D|* O|* }D501 - 601
12X-RAY DIFFRACTION4{ D|* O|* }O1

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