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- PDB-8cuh: Crystal structure of human TEAD2 complexed with its inhibitor TM2. -

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Basic information

Entry
Database: PDB / ID: 8cuh
TitleCrystal structure of human TEAD2 complexed with its inhibitor TM2.
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / Transcription factor / 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 / disordered domain specific binding / sequence-specific double-stranded DNA 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 / chromatin / regulation of DNA-templated transcription / 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
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-P0I / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, S. / Luo, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Elife / Year: 2022
Title: Discovery of a new class of reversible TEA-domain transcription factor inhibitors with a novel binding mode.
Authors: Hu, L. / Sun, Y. / Liu, S. / Erb, H. / Singh, A. / Mao, J. / Luo, X. / Wu, X.
History
DepositionMay 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: 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

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)55,8494
Polymers54,9782
Non-polymers8712
Water54030
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9252
Polymers27,4891
Non-polymers4361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9252
Polymers27,4891
Non-polymers4361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.071, 62.285, 79.914
Angle α, β, γ (deg.)90.00, 117.70, 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-P0I / 4-[3-(2-cyclohexylethoxy)benzoyl]-N-phenylpiperazine-1-carboxamide


Mass: 435.559 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H33N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1 M Hepes, pH 7.2, 2.4 M sodium formate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 20774 / % possible obs: 97 % / Redundancy: 3.6 % / CC1/2: 0.72 / Rpim(I) all: 0.03 / Rsym value: 0.05 / Net I/σ(I): 24.1
Reflection shellResolution: 2.4→2.44 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 863 / CC1/2: 0.72 / Rpim(I) all: 0.46 / Rrim(I) all: 0.82 / Rsym value: 0.68 / % possible all: 83.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HGU

5hgu


Resolution: 2.4→38.925 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 861 4.95 %
Rwork0.1838 --
obs0.1864 17402 81.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→38.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 32 30 3393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083443
X-RAY DIFFRACTIONf_angle_d1.0994642
X-RAY DIFFRACTIONf_dihedral_angle_d11.3562044
X-RAY DIFFRACTIONf_chiral_restr0.055495
X-RAY DIFFRACTIONf_plane_restr0.006591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.54390.3588600.24551315X-RAY DIFFRACTION39
2.5439-2.74030.32881120.25072165X-RAY DIFFRACTION64
2.7403-3.0160.31081490.24042934X-RAY DIFFRACTION87
3.016-3.45220.2631640.20343352X-RAY DIFFRACTION99
3.4522-4.34840.21771880.15593356X-RAY DIFFRACTION99
4.3484-38.90.18981880.16033419X-RAY DIFFRACTION98
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)
14.594-0.7406-2.34085.1533-2.67624.75760.13640.7078-0.0459-0.2720.65431.0014-0.1938-0.2496-0.72370.34850.04630.01870.54790.02120.4601-17.940819.56190.4803
23.51570.8975-4.12692.1304-2.38119.80680.2776-0.48140.32520.31780.2030.4015-0.30650.5641-0.40.190.05710.0250.1868-0.02250.3658-12.288617.811291.8184
36.34691.64282.84822.775-0.06555.1290.333-0.7358-0.6420.3143-0.1075-0.2660.8493-0.0574-0.23470.29870.0187-0.01350.3139-0.00650.1683-6.4673-14.242698.7088
46.11540.9081-0.54473.35570.50514.10010.1542-0.611-0.79740.5133-0.23960.40771.6031-0.89650.06320.5068-0.10230.08860.2693-0.0050.2375-17.3276-18.916892.0832
53.7509-0.3868-0.16823.0225-0.02124.8366-0.24450.37880.6162-0.5528-0.0017-0.285-0.46541.07460.20070.3172-0.0567-0.05010.30780.04080.29262.0066-8.797187.4529
65.25750.32765.22420.60390.37138.39180.0149-0.8707-0.20920.33250.2704-0.1014-0.2328-0.4219-0.26780.4252-0.0035-0.03240.427-0.09760.1524-11.4644-8.5133101.5091
72.22410.46760.93543.14611.16152.2105-0.4391-0.40720.1775-0.26660.26210.2083-0.07980.1549-0.02630.51050.1862-0.10080.23340.02110.2939-7.553-0.401390.3636
83.9740.3934.21760.5480.26739.0781-0.1041-1.2763-0.28220.1222-0.02-0.10260.2222-1.00850.15460.29950.10050.0830.7038-0.01170.2872-14.2375-8.2403104.4096
95.73310.6003-1.03692.24826.73882.422-0.03250.84830.1186-0.7755-0.03971.0459-0.5429-1.22540.3060.3840.008-0.00270.38830.05890.213-16.9857-10.313775.9789
103.54891.05432.45153.82982.633110.0537-0.0282-0.1508-0.0060.0070.0994-0.36090.08720.1119-0.07590.17250.0426-0.00890.09450.01440.2015-4.2579-8.624187.1918
117.20053.760.65346.61011.31774.0577-0.14320.4101-1.2189-0.28620.5952-0.40240.52390.364-0.36240.54290.10250.01470.1575-0.02960.297-2.928-20.766687.4699
122.00021.99951.99981.99972.00012.0004-0.2197-0.39681.86040.1467-3.16361.95211.8679-1.51953.34690.14961.0375-1.2421.0690.03610.296318.6888-9.221991.2701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 222 through 293 )
2X-RAY DIFFRACTION2chain 'A' and (resid 294 through 446 )
3X-RAY DIFFRACTION3chain 'B' and (resid 219 through 238 )
4X-RAY DIFFRACTION4chain 'B' and (resid 239 through 267 )
5X-RAY DIFFRACTION5chain 'B' and (resid 268 through 325 )
6X-RAY DIFFRACTION6chain 'B' and (resid 326 through 339 )
7X-RAY DIFFRACTION7chain 'B' and (resid 340 through 362 )
8X-RAY DIFFRACTION8chain 'B' and (resid 363 through 380 )
9X-RAY DIFFRACTION9chain 'B' and (resid 381 through 395 )
10X-RAY DIFFRACTION10chain 'B' and (resid 396 through 430 )
11X-RAY DIFFRACTION11chain 'B' and (resid 431 through 446 )
12X-RAY DIFFRACTION12chain 'B' and (resid 447 through 447 )

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