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- PDB-8rxq: TEAD2 with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 8rxq
TitleTEAD2 with an inhibitor
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / 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 / Formation of axial mesoderm / regulation of stem cell differentiation / 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 / Formation of axial mesoderm / regulation of stem cell differentiation / embryonic heart tube morphogenesis / embryonic organ development / vasculogenesis / 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 / regulation of transcription by RNA polymerase II / chromatin / 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
: / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsGuichou, J.F. / Gelin, M. / Allemand, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: TEAD2 with an inhibitor
Authors: Guichou, J.F. / Gelin, M. / Allemand, F.
History
DepositionFeb 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Transcriptional enhancer factor TEF-4
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3003
Polymers54,9782
Non-polymers3211
Water00
1
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8102
Polymers27,4891
Non-polymers3211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcriptional enhancer factor TEF-4


Theoretical massNumber of molelcules
Total (without water)27,4891
Polymers27,4891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.135, 61.309, 80.186
Angle α, β, γ (deg.)90.00, 117.42, 90.00
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: 27489.096 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-A1H3X / ethyl (~{E})-3-(5-phenylmethoxy-1~{H}-indol-3-yl)prop-2-enoate


Mass: 321.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19NO3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 2.8M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9697 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9697 Å / Relative weight: 1
ReflectionResolution: 2.63→54.65 Å / Num. obs: 26769 / % possible obs: 94.77 % / Redundancy: 1.8 % / CC1/2: 0.985 / CC star: 0.996 / Net I/σ(I): 5.68
Reflection shellResolution: 2.63→2.72 Å / Num. unique obs: 2647 / CC1/2: 0.586 / CC star: 0.859

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→54.65 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.269 1338 5 %
Rwork0.22 --
obs0.2225 26769 86.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→54.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 24 0 3377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093460
X-RAY DIFFRACTIONf_angle_d1.0794672
X-RAY DIFFRACTIONf_dihedral_angle_d9.946458
X-RAY DIFFRACTIONf_chiral_restr0.054499
X-RAY DIFFRACTIONf_plane_restr0.009599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.730.41351380.38772430X-RAY DIFFRACTION82
2.73-2.830.3751320.36072547X-RAY DIFFRACTION87
2.83-2.960.44481270.34062595X-RAY DIFFRACTION88
2.96-3.120.38671570.32112671X-RAY DIFFRACTION91
3.12-3.310.27211220.272608X-RAY DIFFRACTION89
3.32-3.570.33741420.22342526X-RAY DIFFRACTION86
3.57-3.930.24541270.20832575X-RAY DIFFRACTION88
3.93-4.50.2361440.16642526X-RAY DIFFRACTION86
4.5-5.660.18971410.16492552X-RAY DIFFRACTION87
5.67-54.650.26311080.19792401X-RAY DIFFRACTION81
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)
15.34681.47863.6193.06680.79166.23750.3218-0.3652-0.52930.4222-0.1481-0.28580.6656-0.0218-0.22820.60770.04050.03960.42510.05210.5781-32.5335-16.966322.8826
24.78823.3356-1.79572.5599-0.80141.5725-0.78881.78761.1119-1.35810.68340.0780.1810.55470.03880.7936-0.1795-0.15881.05170.19310.9342-18.2639-2.51218.6372
33.77041.59031.32832.96841.09846.44360.0060.51620.0173-0.0066-0.0077-0.06070.63450.2912-0.20760.69750.02110.04520.44090.01990.5259-32.4052-16.706116.7521
44.06780.63680.70332.43140.74725.87750.1526-0.59360.35370.2831-0.15360.0552-0.598-0.71660.04360.50730.09420.0360.5432-0.04580.5253-35.5781-6.570327.6061
53.21870.63851.56071.21511.60796.31540.1526-0.0131-0.1504-0.22190.1256-0.26210.0473-0.0643-0.11860.60830.00840.06630.43050.02420.6016-31.5669-13.520814.0023
67.5370.9376-1.62883.6539-0.50926.68860.58420.01190.4016-0.3963-0.17410.0545-0.84650.1674-0.11270.68260.15010.08860.42910.01760.6149-39.056720.954922.2864
73.1631-2.04841.17111.6752-0.90430.4958-0.34251.246-1.3432-1.25090.59640.16690.960.04050.25281.0077-0.0940.19080.9559-0.03941.1767-51.78218.815915.0636
84.65230.2993-3.62261.9976-1.08497.53030.1338-0.35890.27390.0161-0.02380.0023-0.0770.4712-0.12260.58760.0471-0.00010.3774-0.00270.5311-36.915715.671521.1134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 218 through 277 )
2X-RAY DIFFRACTION2chain 'B' and (resid 278 through 293 )
3X-RAY DIFFRACTION3chain 'B' and (resid 294 through 325 )
4X-RAY DIFFRACTION4chain 'B' and (resid 326 through 380 )
5X-RAY DIFFRACTION5chain 'B' and (resid 381 through 446 )
6X-RAY DIFFRACTION6chain 'A' and (resid 222 through 277 )
7X-RAY DIFFRACTION7chain 'A' and (resid 278 through 293 )
8X-RAY DIFFRACTION8chain 'A' and (resid 294 through 446 )

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