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- PDB-8ryc: TEAD2 with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 8ryc
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
: / MYRISTIC ACID / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 8, 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
A: Transcriptional enhancer factor TEF-4
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4304
Polymers54,9782
Non-polymers4522
Water1,22568
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7122
Polymers27,4891
Non-polymers2231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7172
Polymers27,4891
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.295, 61.445, 79.932
Angle α, β, γ (deg.)90.00, 117.49, 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-A1H32 / 5-phenylmethoxy-1~{H}-indole


Mass: 223.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13NO
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.59 %
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: 2.09→70.91 Å / Num. obs: 31749 / % possible obs: 99.59 % / Redundancy: 3 % / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 8.98
Reflection shellResolution: 2.09→2.16 Å / Num. unique obs: 3133 / CC1/2: 0.723 / CC star: 0.916

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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: 2.09→70.91 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 1585 5 %
Rwork0.2089 --
obs0.211 31727 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→70.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 31 68 3527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083585
X-RAY DIFFRACTIONf_angle_d0.9874857
X-RAY DIFFRACTIONf_dihedral_angle_d7.707507
X-RAY DIFFRACTIONf_chiral_restr0.055515
X-RAY DIFFRACTIONf_plane_restr0.009650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.160.38821250.33042689X-RAY DIFFRACTION98
2.16-2.230.34871560.30212718X-RAY DIFFRACTION100
2.23-2.320.33181340.26622725X-RAY DIFFRACTION100
2.32-2.430.27791510.24682732X-RAY DIFFRACTION100
2.43-2.560.29221360.25422750X-RAY DIFFRACTION100
2.56-2.720.34471300.26352739X-RAY DIFFRACTION99
2.72-2.930.29331490.23672717X-RAY DIFFRACTION99
2.93-3.220.25871500.22862738X-RAY DIFFRACTION100
3.22-3.690.2411410.19522770X-RAY DIFFRACTION100
3.69-4.650.22581550.16122757X-RAY DIFFRACTION100
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)
13.7585-0.5183-5.58944.351.50158.26960.2745-0.98271.13780.20120.24930.2843-0.77370.1251-0.44280.50610.00750.08010.3643-0.00270.293540.024152.6839-7.6435
25.9288-1.8692-0.3047.36012.2497.7212-0.0922-1.14291.08690.66360.37770.326-0.86580.2245-0.18680.5965-0.04580.2020.3917-0.08720.535244.087459.557-10.6159
33.91031.2099-1.38714.3651-0.24456.33030.01410.38050.0382-0.56170.14840.39770.1283-0.6404-0.12080.44410.05630.03730.29520.05070.418734.989948.1891-21.0233
43.58860.1347-2.95161.1774-0.47656.383-0.0039-0.40230.0220.17320.13710.16350.08040.3462-0.12570.38720.05620.02190.23480.01070.322243.056347.4256-14.1797
50.63181.22920.14263.46391.16083.91870.2865-0.7188-0.32950.1229-0.25660.0860.6576-0.8667-0.08310.3241-0.08290.06310.3963-0.00670.246942.695515.127-10.6772
67.63770.12293.60381.58381.36566.5473-0.21470.3835-0.2947-0.09450.3294-0.3949-0.06110.8739-0.17090.3780.0160.05850.32760.02760.325556.457518.7918-16.0839
73.03640.60951.47031.05251.20656.2786-0.0457-0.3050.2135-0.11460.0043-0.0374-0.41-0.42850.07910.45110.08090.06450.2610.04120.329546.228823.7634-14.8651
84.6766.2012.27728.85391.30396.1038-0.1410.2605-1.5205-0.14470.5022-0.6930.38260.5659-0.28140.39260.0920.0540.3115-0.05250.405954.036910.5652-18.4816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 221 through 238 )
2X-RAY DIFFRACTION2chain 'A' and (resid 239 through 267 )
3X-RAY DIFFRACTION3chain 'A' and (resid 268 through 325 )
4X-RAY DIFFRACTION4chain 'A' and (resid 326 through 446 )
5X-RAY DIFFRACTION5chain 'B' and (resid 217 through 255 )
6X-RAY DIFFRACTION6chain 'B' and (resid 256 through 325 )
7X-RAY DIFFRACTION7chain 'B' and (resid 326 through 430 )
8X-RAY DIFFRACTION8chain 'B' and (resid 431 through 447 )

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