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- PDB-8zbh: Crystal structure of TEAD3 YAP binding domain with compound 3 -

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Basic information

Entry
Database: PDB / ID: 8zbh
TitleCrystal structure of TEAD3 YAP binding domain with compound 3
ComponentsTranscriptional enhancer factor TEF-5
KeywordsTRANSCRIPTION / transcription factor / TEAD3
Function / homology
Function and homology information


asymmetric neuroblast division / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / embryonic organ development / female pregnancy / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...asymmetric neuroblast division / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / embryonic organ development / female pregnancy / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Transcriptional enhancer factor TEF-5 (TEAD3) / 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-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYoo, Y. / Kim, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Pan-Transcriptional Enhanced Associated Domain Palmitoylation Pocket Covalent Inhibitor.
Authors: Kim, J. / Kim, H. / Kim, J. / Cho, S.Y. / Moon, S. / Yoo, Y. / Kim, H. / Kim, J.K. / Jeon, H. / Namkung, W. / Han, G. / No, K.T.
History
DepositionApr 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-5
B: Transcriptional enhancer factor TEF-5
C: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1886
Polymers76,1883
Non-polymers1,0003
Water70339
1
A: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7292
Polymers25,3961
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7292
Polymers25,3961
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7292
Polymers25,3961
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.170, 101.740, 149.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Transcriptional enhancer factor TEF-5 / DTEF-1 / TEA domain family member 3 / TEAD-3


Mass: 25395.867 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD3, TEAD5, TEF5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99594
#2: Chemical ChemComp-A1L1O / 1-[7-[4-(trifluoromethyl)phenyl]-3,4-dihydro-1~{H}-isoquinolin-2-yl]propan-1-one


Mass: 333.348 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H18F3NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 0.2M Ammonium acetate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→28.17 Å / Num. obs: 22344 / % possible obs: 99.82 % / Redundancy: 2 % / Biso Wilson estimate: 53.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03486 / Net I/σ(I): 15.12
Reflection shellResolution: 2.6→2.693 Å / Rmerge(I) obs: 0.3577 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 2194 / CC1/2: 0.806

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
ELVESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→28.17 Å / SU ML: 0.3577 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3782
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2702 1118 5 %
Rwork0.2119 21222 -
obs0.2148 22340 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.16 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 72 39 5379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01035474
X-RAY DIFFRACTIONf_angle_d1.33427401
X-RAY DIFFRACTIONf_chiral_restr0.064794
X-RAY DIFFRACTIONf_plane_restr0.0086939
X-RAY DIFFRACTIONf_dihedral_angle_d16.91182020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.35221370.32042605X-RAY DIFFRACTION99.96
2.72-2.860.37191370.28382599X-RAY DIFFRACTION100
2.86-3.040.35511370.27622600X-RAY DIFFRACTION99.85
3.04-3.270.32561390.25242641X-RAY DIFFRACTION99.96
3.28-3.60.26641380.22142621X-RAY DIFFRACTION99.96
3.6-4.120.24471390.19282645X-RAY DIFFRACTION100
4.12-5.190.23171420.16292697X-RAY DIFFRACTION99.96
5.19-28.170.23991490.19862814X-RAY DIFFRACTION99.73

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