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- PDB-8e1o: Crystal structure of hTEAD2 bound to a methoxypyridine lipid pock... -

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Basic information

Entry
Database: PDB / ID: 8e1o
TitleCrystal structure of hTEAD2 bound to a methoxypyridine lipid pocket binder
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION/INHIBITOR / Transcription factor inhibitor complex / TRANSCRIPTION-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-Y2S / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsNoland, C.L. / Dey, A. / Zbieg, J. / Crawford, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2024
Title: Targeting the Hippo pathway in cancers via ubiquitination dependent TEAD degradation
Authors: Pham, T. / Pahuja, K. / Hagenbeek, T. / Zbieg, Z. / Noland, C.L. / Pham, V.C. / Yao, X. / Rose, C. / Browder, K. / Lee, H.J. / Yu, M. / Chu, M.L. / Martin, S. / Verschueren, E. / Li, J. / ...Authors: Pham, T. / Pahuja, K. / Hagenbeek, T. / Zbieg, Z. / Noland, C.L. / Pham, V.C. / Yao, X. / Rose, C. / Browder, K. / Lee, H.J. / Yu, M. / Chu, M.L. / Martin, S. / Verschueren, E. / Li, J. / Kubala, M. / Fong, R. / Lorenzo, M. / Beroza, P. / Hsu, P. / Paul, S. / Villemure, E. / Lee, W. / Cheung, T. / Clausen, S. / Lacap, J. / Liang, Y. / Schmidt, S. / Modrusan, Z. / Cohen, M. / Crawford, J. / Jasper, H. / Ashworth, A. / Lill, J.R. / Malek, S. / Rudolph, J. / Wertz, I. / Chang, M. / Ye, X. / Dey, A.
History
DepositionAug 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year

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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)58,1315
Polymers57,0302
Non-polymers1,1013
Water39622
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1273
Polymers28,5151
Non-polymers6122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0052
Polymers28,5151
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.150, 62.069, 79.856
Angle α, β, γ (deg.)90.000, 117.410, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 28515.121 Da / Num. of mol.: 2 / Mutation: UNP residues 217-447
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-Y2S / 5-methoxy-N-({3-[2-(methylamino)-2-oxoethyl]phenyl}methyl)-4-{(E)-2-[trans-4-(trifluoromethyl)cyclohexyl]ethenyl}pyridine-2-carboxamide


Mass: 489.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H30F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM potassium/sodium tartrate, pH 6.5, 20% PEG3350

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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: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→70.89 Å / Num. obs: 14901 / % possible obs: 92.3 % / Redundancy: 3.3 % / CC1/2: 0.998 / Net I/σ(I): 10.6
Reflection shellResolution: 2.25→2.55 Å / Num. unique obs: 745 / CC1/2: 0.643

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.27data extraction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMV

5emv


Resolution: 2.25→70.89 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 713 4.79 %
Rwork0.2003 14186 -
obs0.2026 14899 58.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.2 Å2 / Biso mean: 46.6802 Å2 / Biso min: 22.24 Å2
Refinement stepCycle: final / Resolution: 2.25→70.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 78 22 3275
Biso mean--39.24 38.81 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063336
X-RAY DIFFRACTIONf_angle_d0.7294522
X-RAY DIFFRACTIONf_dihedral_angle_d20.791170
X-RAY DIFFRACTIONf_chiral_restr0.043494
X-RAY DIFFRACTIONf_plane_restr0.003572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.420.3516170.3586273X-RAY DIFFRACTION6
2.43-2.670.3459550.29871074X-RAY DIFFRACTION22
2.67-3.060.30611620.29093148X-RAY DIFFRACTION66
3.06-3.850.28862270.20744817X-RAY DIFFRACTION99
3.85-70.890.20642520.17054874X-RAY DIFFRACTION99
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)
10.59170.2626-0.63654.681-0.43022.13330.5153-0.4329-0.0607-0.0598-0.2978-0.09620.6516-0.66310.00160.3301-0.04040.00360.5003-0.03710.06-36.9002-21.418926.0289
22.83120.47652.25381.44131.74942.4497-0.20620.3872-0.0012-0.18490.1875-0.5217-0.01280.875600.35280.00550.01450.55210.03750.4704-22.9885-16.440819.1943
32.931-0.2518-1.25731.2489-1.22591.89140.0527-0.29230.1891-0.203-0.1912-0.10130.0694-0.1612-0.00230.37110.10070.00610.1987-0.01730.2261-33.057-18.21323.4994
41.3960.46820.34340.97030.29081.095-0.2432-0.1870.3656-0.3237-0.4140.2206-0.85480.1595-0.03840.38620.1911-0.10330.3383-0.02230.473-32.2731-6.290520.2049
53.65250.33780.0131.5232-0.58182.7626-0.0818-0.3420.2345-0.0618-0.101-0.0413-0.0856-0.4659-0.00240.29580.11450.02520.27240.02710.2929-34.3305-14.851318.3815
67.98244.03173.31795.87612.03164.9683-0.33190.8797-0.0928-0.41340.5991-0.23060.49920.80510.18490.53580.2162-0.08790.24220.08330.2864-27.1608-26.592416.7567
73.8131-0.7971-1.80983.7195-3.0792.3219-0.09660.6691-0.2636-0.02950.66850.8258-0.1827-0.42970.0030.36390.04730.05730.57530.0710.5279-42.474813.867720.2863
82.2224-0.0573-1.76572.0777-1.8265.91390.0179-0.3551-0.17550.13830.2560.2395-0.13930.23270.00480.29990.0492-0.01040.23840.05570.3891-36.612211.715720.9668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 217 through 248 )A217 - 248
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 293 )A249 - 293
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 339 )A294 - 339
4X-RAY DIFFRACTION4chain 'A' and (resid 340 through 362 )A340 - 362
5X-RAY DIFFRACTION5chain 'A' and (resid 363 through 430 )A363 - 430
6X-RAY DIFFRACTION6chain 'A' and (resid 431 through 446 )A431 - 446
7X-RAY DIFFRACTION7chain 'B' and (resid 222 through 293 )B222 - 293
8X-RAY DIFFRACTION8chain 'B' and (resid 294 through 446 )B294 - 446

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