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- PDB-6uyb: Crystal structure of TEAD2 bound to Compound 1 -

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Basic information

Entry
Database: PDB / ID: 6uyb
TitleCrystal structure of TEAD2 bound to Compound 1
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTranscription/Transcription Inhibitor / EAD / YAP Binding Domain / Transcription Inhibitor / Palmitoylation inhibitor / Transcription-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
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-QSJ / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.543 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)54,3686
Polymers53,4062
Non-polymers9624
Water3,495194
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1693
Polymers26,7031
Non-polymers4662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1993
Polymers26,7031
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.418, 62.090, 79.620
Angle α, β, γ (deg.)90.000, 117.820, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-QSJ / (3R,4R)-1-{3-[(E)-2-(4-chlorophenyl)ethenyl]-4-methoxy-5-methylphenyl}-3,4-dihydroxypyrrolidin-2-one


Mass: 373.830 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20ClNO4 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.59 Å3/Da / Density % sol: 52.42 %
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: 0.999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.543→70.417 Å / Num. obs: 39934 / % possible obs: 86 % / Redundancy: 3.3 % / CC1/2: 0.999 / Net I/σ(I): 13
Reflection shellResolution: 1.543→1.71 Å / Num. unique obs: 1997 / CC1/2: 0.609

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
ADDREFdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMV

5emv


Resolution: 1.543→70.417 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.63
RfactorNum. reflection% reflection
Rfree0.2319 2001 5.01 %
Rwork0.1958 --
obs0.1976 39913 50.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.8 Å2 / Biso mean: 32.1939 Å2 / Biso min: 7.67 Å2
Refinement stepCycle: final / Resolution: 1.543→70.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 66 198 3503
Biso mean--38.32 36.96 -
Num. residues----402
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5431-1.58170.149150.26661342
1.5817-1.62440.461210.27693947
1.6244-1.67220.2948280.258265512
1.6722-1.72620.2585560.2785109120
1.7262-1.78790.3243870.2648152529
1.7879-1.85950.31341030.2713203438
1.8595-1.94420.31931220.2827186035
1.9442-2.04670.26461800.2343317260
2.0467-2.17490.25931550.2243311458
2.1749-2.34280.30942150.2459352667
2.3428-2.57860.26322900.2155531899
2.5786-2.95170.26932340.2116496992
2.9517-3.71890.20972290.178487790
3.7189-70.4170.18082760.1604524395
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)
10.4163-0.0799-0.35040.8060.0880.62680.0617-0.34840.03470.12050.0424-0.1158-0.2444-0.1281.0230.1528-0.0358-0.02120.3126-0.03650.1289-36.3693-14.448630.3301
21.1723-0.5256-0.88620.84250.47233.82250.2174-0.08310.3443-0.01970.2546-0.2148-0.5532-0.06580.45170.21660.03170.00610.0985-0.00480.1423-32.213-6.822518.9382
30.85680.70990.51710.74410.9081.78610.1412-0.5385-0.31590.09490.1165-0.13640.1389-0.49380.25050.14070.077-0.02420.4222-0.02360.1361-39.2883-13.893533.4026
41.0479-0.5044-0.20081.55720.38034.36720.10480.1576-0.0164-0.1436-0.07110.16180.3379-0.49640.15620.13930.00810.0060.0405-0.00050.0872-36.0612-16.89487.8438
52.243-0.6773-0.36261.8461-0.51762.24090.0068-0.1127-0.03190.00550.0557-0.05640.14820.14820.0887-0.0136-0.0256-0.0538-0.1272-0.04280.0193-27.7459-19.628319.8701
62.01762.022-0.18923.4405-1.32591.12480.072-0.77480.7820.44440.13420.2496-0.170.30460.63630.16260.0162-0.00250.256-0.04250.1254-39.594615.726227.8247
70.6294-0.1312-0.79791.811-0.53811.28990.21990.53920.3125-0.05120.01810.4596-0.1359-0.2330.03340.19220.0326-0.02010.3609-0.01480.3191-40.113216.747616.366
83.7593-1.57441.23913.7315-4.66315.99960.16760.8184-1.2632-0.9104-0.21720.56971.30550.1820.1370.3931-0.0749-0.04840.4859-0.13050.5611-52.2314.433414.3523
92.2327-0.18-0.61522.0107-0.07461.86080.1063-0.43420.17910.17920.0076-0.0145-0.04030.31370.23930.13790.02170.02080.1813-0.02480.176-38.388314.498424.157
100.5761-0.1844-0.52680.41040.05521.8251-0.0197-0.1498-0.00070.0540.31350.10340.294-0.02940.08830.34630.07620.0610.14640.02330.1798-39.83612.429521.5104
115.0111-0.6494-4.27440.13980.62493.74450.0865-1.07390.3310.06540.1768-0.0609-0.03130.88640.35370.29780.02960.01620.46040.02060.1749-36.956411.42835.7709
122.1474-0.28161.09324.0153-0.10093.8248-0.07590.0887-0.2638-0.2442-0.0478-0.8810.14960.96272.12330.13920.021-0.0050.2182-0.00250.2067-24.34769.598811.2264
131.4673-0.1518-0.78451.28570.00422.28010.2598-0.13040.3566-0.06540.07420.1194-0.350.26160.14930.19060.00070.01030.0577-0.00480.1037-36.146311.849711.3545
141.90910.21980.9692.21950.99851.0709-0.2-0.3522-0.34830.14920.00050.14260.4343-0.2598-1.1310.10330.03910.02180.08320.05450.1437-45.06039.072422.1767
153.8631.0569-0.28742.282-0.33671.7563-0.15850.10970.2778-0.07010.32570.1049-0.2892-0.10180.08740.2070.030.01910.08540.03450.3396-40.423422.680515.3502
160.87431.1907-0.98283.31040.21832.54140.0842-0.7318-0.15750.63150.0532-1.10090.39490.9201-0.97340.09210.0367-0.1380.3646-0.00470.2282-20.767-21.309832.2088
171.5215-0.08750.38970.86490.00611.41340.327-0.7114-0.16360.0112-0.22240.21240.4123-1.01340.81740.1463-0.1224-0.04270.4267-0.02140.1169-47.4719-21.540622.2144
180.63340.3949-0.15920.86170.36761.4434-0.0268-0.1001-0.3874-0.05660.0369-0.36420.39570.3644-0.11460.14530.0509-0.01970.21990.03770.2502-25.1441-22.607518.6983
190.836-1.1509-0.26292.3326-0.24532.6534-0.10550.04630.2172-0.33890.029-0.2525-0.29820.38320.0640.0787-0.0381-0.02590.0660.01070.0415-25.7328-15.47217.4596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 326 through 339 )B326 - 339
2X-RAY DIFFRACTION2chain 'B' and (resid 340 through 362 )B340 - 362
3X-RAY DIFFRACTION3chain 'B' and (resid 363 through 380 )B363 - 380
4X-RAY DIFFRACTION4chain 'B' and (resid 381 through 414 )B381 - 414
5X-RAY DIFFRACTION5chain 'B' and (resid 415 through 446 )B415 - 446
6X-RAY DIFFRACTION6chain 'A' and (resid 222 through 238 )A222 - 238
7X-RAY DIFFRACTION7chain 'A' and (resid 246 through 277 )A246 - 277
8X-RAY DIFFRACTION8chain 'A' and (resid 278 through 293 )A278 - 293
9X-RAY DIFFRACTION9chain 'A' and (resid 294 through 339 )A294 - 339
10X-RAY DIFFRACTION10chain 'A' and (resid 340 through 362 )A340 - 362
11X-RAY DIFFRACTION11chain 'A' and (resid 363 through 380 )A363 - 380
12X-RAY DIFFRACTION12chain 'A' and (resid 381 through 395 )A381 - 395
13X-RAY DIFFRACTION13chain 'A' and (resid 396 through 414 )A396 - 414
14X-RAY DIFFRACTION14chain 'A' and (resid 415 through 430 )A415 - 430
15X-RAY DIFFRACTION15chain 'A' and (resid 431 through 446 )A431 - 446
16X-RAY DIFFRACTION16chain 'B' and (resid 217 through 228 )B217 - 228
17X-RAY DIFFRACTION17chain 'B' and (resid 229 through 248 )B229 - 248
18X-RAY DIFFRACTION18chain 'B' and (resid 249 through 277 )B249 - 277
19X-RAY DIFFRACTION19chain 'B' and (resid 278 through 325 )B278 - 325

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