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- PDB-8a0v: Crystal structure of TEAD3 in complex with CPD2 -

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Basic information

Entry
Database: PDB / ID: 8a0v
TitleCrystal structure of TEAD3 in complex with CPD2
ComponentsTranscriptional enhancer factor TEF-5
KeywordsTRANSCRIPTION / Inhibitor / Complex
Function / homology
Function and homology information


RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / asymmetric neuroblast division / hippo signaling / positive regulation of stem cell population maintenance / embryonic organ development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / asymmetric neuroblast division / hippo signaling / positive regulation of stem cell population maintenance / embryonic organ development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / 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 / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
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
Chem-KNE / MYRISTIC ACID / PHOSPHATE ION / Transcriptional enhancer factor TEF-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsScheufler, C. / Kallen, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemmedchem / Year: 2022
Title: The First Class of Small Molecules Potently Disrupting the YAP-TEAD Interaction by Direct Competition.
Authors: Furet, P. / Bordas, V. / Le Douget, M. / Salem, B. / Mesrouze, Y. / Imbach-Weese, P. / Sellner, H. / Voegtle, M. / Soldermann, N. / Chapeau, E. / Wartmann, M. / Scheufler, C. / Fernandez, C. ...Authors: Furet, P. / Bordas, V. / Le Douget, M. / Salem, B. / Mesrouze, Y. / Imbach-Weese, P. / Sellner, H. / Voegtle, M. / Soldermann, N. / Chapeau, E. / Wartmann, M. / Scheufler, C. / Fernandez, C. / Kallen, J. / Guagnano, V. / Chene, P. / Schmelzle, T.
History
DepositionMay 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 19, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
D: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,61123
Polymers101,3354
Non-polymers3,27619
Water4,522251
1
A: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3507
Polymers25,3341
Non-polymers1,0166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2726
Polymers25,3341
Non-polymers9385
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9955
Polymers25,3341
Non-polymers6614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9955
Polymers25,3341
Non-polymers6614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.094, 128.945, 156.709
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 25333.842 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Tead3, Tcf13r2, Tef5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P70210

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Non-polymers , 5 types, 270 molecules

#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-KNE / [(2~{S})-5-chloranyl-2-phenyl-3~{H}-1-benzofuran-2-yl]methanamine


Mass: 259.731 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H14ClNO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.1 - 1.4 M sodium/potassium phosphate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.699→48.413 Å / Num. obs: 35648 / % possible obs: 96.1 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Net I/σ(I): 13
Reflection shellResolution: 2.699→2.771 Å / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1782 / CC1/2: 0.816 / % possible all: 64.1

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (3-FEB-2022)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house structure

Resolution: 2.699→35.87 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.574 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.611 / SU Rfree Blow DPI: 0.294 / SU Rfree Cruickshank DPI: 0.295
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 1781 -RANDOM
Rwork0.2053 ---
obs0.2072 35636 96.1 %-
Displacement parametersBiso mean: 42.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.867 Å20 Å20 Å2
2--1.6477 Å20 Å2
3----3.5146 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.699→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6759 0 150 251 7160
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087107HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.979599HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2445SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1166HARMONIC5
X-RAY DIFFRACTIONt_it7107HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion891SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4912SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion16.93
LS refinement shellResolution: 2.7→2.73 Å
RfactorNum. reflection% reflection
Rfree0.3112 32 -
Rwork0.2518 --
obs0.2544 713 58.3 %
Refinement TLS params.

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)
10.56930.1599-0.09011.6759-0.12942.5307-0.03610.0008-0.11040.0008-0.0291-0.0937-0.1104-0.09370.0652-0.15530.03-0.00370.05110.005-0.11060.8912-4.3774-21.145
21.624-0.2567-0.0651.2393-0.03851.407-0.0665-0.04610.0335-0.04610.06780.13450.03350.1345-0.0013-0.1274-0.00550.0242-0.01790.0338-0.064326.7618-14.3848-27.0964
30.4530.01640.04191.52460.14512.124-0.0221-0.0348-0.1068-0.0348-0.06230.1696-0.10680.16960.0844-0.1212-0.00990.00340.0184-0.0054-0.075911.0957-0.329113.6993
41.7420.1494-0.03151.4409-0.25571.44-0.00730.0798-0.00960.0798-0.0004-0.1532-0.0096-0.15320.0076-0.10990.02480.0562-0.0171-0.0052-0.0922-15.5018-8.896421.256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* L|* }A219 - 435
2X-RAY DIFFRACTION1{ A|* L|* }A501
3X-RAY DIFFRACTION1{ A|* L|* }L1 - 2
4X-RAY DIFFRACTION2{ B|* M|* }B218 - 435
5X-RAY DIFFRACTION2{ B|* M|* }B501
6X-RAY DIFFRACTION2{ B|* M|* }M1 - 2
7X-RAY DIFFRACTION3{ C|* N|* }C218 - 435
8X-RAY DIFFRACTION3{ C|* N|* }N1
9X-RAY DIFFRACTION4{ D|* O|* }D218 - 434
10X-RAY DIFFRACTION4{ D|* O|* }D501
11X-RAY DIFFRACTION4{ D|* O|* }O1

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