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- PDB-6uyc: Crystal structure of TEAD2 bound to Compound 2 -

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Basic information

Entry
Database: PDB / ID: 6uyc
TitleCrystal structure of TEAD2 bound to Compound 2
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION/INHIBITOR / TEAD / YAP Binding Domain / Transcription Inhibitor / Palmitoylation inhibitor / 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 / embryonic organ development / vasculogenesis / cellular response to retinoic acid / neural tube closure / transcription coactivator binding / disordered domain specific binding / sequence-specific double-stranded DNA 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 / chromatin / regulation of DNA-templated transcription / 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
Coagulation Factor XIII; Chain A, domain 1 - #80 / 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 ...Coagulation Factor XIII; Chain A, domain 1 - #80 / 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 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-QLV / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.658 Å
AuthorsNoland, C.L. / Holden, J.K. / Crawford, J.J. / Zbieg, J.R. / Cunningham, C.N.
CitationJournal: Cell Rep / Year: 2020
Title: Small Molecule Dysregulation of TEAD Lipidation Induces a Dominant-Negative Inhibition of Hippo Pathway Signaling.
Authors: Holden, J.K. / Crawford, J.J. / Noland, C.L. / Schmidt, S. / Zbieg, J.R. / Lacap, J.A. / Zang, R. / Miller, G.M. / Zhang, Y. / Beroza, P. / Reja, R. / Lee, W. / Tom, J.Y.K. / Fong, R. / ...Authors: Holden, J.K. / Crawford, J.J. / Noland, C.L. / Schmidt, S. / Zbieg, J.R. / Lacap, J.A. / Zang, R. / Miller, G.M. / Zhang, Y. / Beroza, P. / Reja, R. / Lee, W. / Tom, J.Y.K. / Fong, R. / Steffek, M. / Clausen, S. / Hagenbeek, T.J. / Hu, T. / Zhou, Z. / Shen, H.C. / Cunningham, C.N.
History
DepositionNov 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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)54,2215
Polymers53,4062
Non-polymers8153
Water2,738152
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0502
Polymers26,7031
Non-polymers3461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1723
Polymers26,7031
Non-polymers4692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.422, 61.249, 80.206
Angle α, β, γ (deg.)90.000, 117.260, 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: 26703.135 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-QLV / N-{5-[(E)-2-(4,4-difluorocyclohexyl)ethenyl]-6-methoxypyridin-3-yl}methanesulfonamide


Mass: 346.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20F2N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 51.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM potassium/sodium tartrate pH 6.5 20% 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: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.658→58.241 Å / Num. obs: 36599 / % possible obs: 87.1 % / Redundancy: 3.3 % / CC1/2: 0.999 / Net I/σ(I): 15.7
Reflection shellResolution: 1.661→1.819 Å / Num. unique obs: 1830 / CC1/2: 0.628

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Processing

Software
NameVersionClassification
PHENIXdev_3290refinement
PDB_EXTRACT3.25data extraction
ADDREFdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMV

5emv


Resolution: 1.658→58.241 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.46
Details: Diffraction was moderately anisotropic, with resolution limits of 2.30, 1.82, and 1.66 angstroms along the a, b, and c axes, respectively. The data were therefore elliptically truncated and ...Details: Diffraction was moderately anisotropic, with resolution limits of 2.30, 1.82, and 1.66 angstroms along the a, b, and c axes, respectively. The data were therefore elliptically truncated and corrected using STARANISO.
RfactorNum. reflection% reflection
Rfree0.2163 1739 4.75 %
Rwork0.1937 --
obs0.1949 36599 57.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.51 Å2 / Biso mean: 37.8383 Å2 / Biso min: 13.99 Å2
Refinement stepCycle: final / Resolution: 1.658→58.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 54 152 3457
Biso mean--37.11 40.98 -
Num. residues----404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.658-1.70660.318490.35971573
1.7066-1.76170.3559260.307858212
1.7617-1.82460.29550.2896114923
1.8246-1.89770.3109880.2783156431
1.8977-1.98410.2491950.2512160032
1.9841-2.08870.26731210.2513268353
2.0887-2.21950.24072160.231396780
2.2195-2.39090.2861780.2305399579
2.3909-2.63150.27072490.2364992100
2.6315-3.01230.28082200.2198462992
3.0123-3.79510.19352210.1715461991
3.7951-58.2410.16372610.1541492396
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)
10.51770.93210.2042.04010.12273.2650.1586-0.5787-0.2381-0.0339-0.0961-0.03020.4267-0.65120.00260.2094-0.0675-0.00990.2718-0.01060.1804-37.5981-20.776325.9629
24.40790.83510.88771.04810.12652.19970.9686-1.3817-1.36210.013-0.017-0.34841.4679-0.69750.2370.4028-0.0093-0.12140.20580.07840.3695-31.7144-25.727624.1066
34.17091.33150.77732.03510.48385.3187-0.5940.67430.0371-0.91040.4154-0.3995-0.4781.0971-0.15890.3117-0.05740.00040.28540.07240.2774-23.177-15.305116.859
41.5068-0.1481-1.17182.59040.67741.34640.087-0.2748-0.00180.27170.0842-0.2554-0.17930.00250.03320.1909-0.0202-0.02720.2923-0.01960.1705-36.0896-13.565930.5244
51.81670.21012.10853.11120.65511.91860.2137-0.01350.1984-0.3220.1552-0.0216-0.467-0.10530.00050.24980.0638-0.02040.18360.00430.2603-32.3708-5.940320.3457
63.3830.19570.56752.03222.04731.4707-0.0661-0.9958-0.13070.27170.009-0.0708-0.1631-0.76-0.00320.16590.00310.01340.43140.00520.2509-38.9084-12.959233.073
71.5089-0.2333-0.06290.8156-0.40621.30830.11780.4537-0.0547-0.5129-0.20740.04070.0072-0.7168-0.00020.32610.03640.00480.35070.00890.2263-41.6123-15.52435.2649
81.62690.50830.66880.2197-0.58941.650.03180.15060.0057-0.24420.0637-0.21720.19350.05610.05980.2890.0520.03830.14440.02260.1899-30.3318-16.309310.517
93.25020.71230.07691.66150.24683.77660.0394-0.1033-0.0847-0.06790.0517-0.23120.15390.30350.06120.1620.048-0.00340.0850.04960.2384-27.1587-18.740620.3269
100.74050.7174-0.64291.8159-0.53732.05670.1016-0.5660.50.20960.07950.087-0.19130.23390.00010.19970.04970.00190.3017-0.01910.2655-39.264815.585828.3727
112.43430.5034-2.89995.172-0.57833.52130.10850.10050.5571-0.00090.19480.4191-0.4986-0.33870.00960.33520.08680.05390.27640.02760.3219-39.113619.438419.1101
121.18720.1813-0.17563.4075-1.33111.1297-0.13191.7409-0.903-1.64220.14671.36760.8786-0.50220.06980.6202-0.0436-0.14710.8575-0.12910.7461-51.14736.323412.9635
131.28690.35680.29623.57890.24584.021-0.0815-0.22010.374-0.17870.0544-0.0552-0.12040.21580.04120.14110.06790.03270.10130.01750.2357-38.191117.286717.7912
140.23930.09860.13730.8999-0.51391.3899-0.0921-0.5770.18210.08270.0926-0.06630.32780.4461-0.00050.29410.060.00860.4115-0.00950.262-38.841411.290132.5491
152.3159-0.4209-1.63153.029-0.40260.8840.0859-0.1689-0.0473-0.12830.18550.07170.29740.0240.00020.33210.0673-0.0130.19580.02010.2658-39.64912.813821.4977
161.26941.3426-1.8110.6467-0.72030.6183-0.0563-0.87440.33710.15570.08480.01630.23041.03890.00040.34080.1541-0.01090.60350.01220.2826-36.994910.83136.013
172.0408-0.60950.62371.18381.32131.8784-0.3904-0.3477-0.3457-0.5233-0.0368-0.27970.71310.978-0.00880.35190.11750.02060.40470.06890.2979-24.0629.304111.035
181.5021-0.3356-0.24230.16230.6371.2268-0.02340.02650.1704-0.21380.19460.24250.0862-0.00110.01720.31850.06240.01110.15490.00650.1993-36.248712.158311.899
192.449-0.31680.54192.7395-0.82324.3021-0.11530.05920.3567-0.06970.33050.2663-0.056-0.36550.04210.14120.067-0.00870.1187-0.00480.2597-42.025616.251719.8741
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 267 )A249 - 267
3X-RAY DIFFRACTION3chain 'A' and (resid 268 through 325 )A268 - 325
4X-RAY DIFFRACTION4chain 'A' and (resid 326 through 339 )A326 - 339
5X-RAY DIFFRACTION5chain 'A' and (resid 340 through 362 )A340 - 362
6X-RAY DIFFRACTION6chain 'A' and (resid 363 through 380 )A363 - 380
7X-RAY DIFFRACTION7chain 'A' and (resid 381 through 395 )A381 - 395
8X-RAY DIFFRACTION8chain 'A' and (resid 396 through 414 )A396 - 414
9X-RAY DIFFRACTION9chain 'A' and (resid 415 through 446 )A415 - 446
10X-RAY DIFFRACTION10chain 'B' and (resid 222 through 238 )B222 - 238
11X-RAY DIFFRACTION11chain 'B' and (resid 239 through 274 )B239 - 274
12X-RAY DIFFRACTION12chain 'B' and (resid 275 through 293 )B275 - 293
13X-RAY DIFFRACTION13chain 'B' and (resid 294 through 325 )B294 - 325
14X-RAY DIFFRACTION14chain 'B' and (resid 326 through 339 )B326 - 339
15X-RAY DIFFRACTION15chain 'B' and (resid 340 through 362 )B340 - 362
16X-RAY DIFFRACTION16chain 'B' and (resid 363 through 380 )B363 - 380
17X-RAY DIFFRACTION17chain 'B' and (resid 381 through 395 )B381 - 395
18X-RAY DIFFRACTION18chain 'B' and (resid 396 through 414 )B396 - 414
19X-RAY DIFFRACTION19chain 'B' and (resid 415 through 446 )B415 - 446

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