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- PDB-7t2l: Crystal Structure of TEAD2 in a covalent complex with TED-662 -

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Basic information

Entry
Database: PDB / ID: 7t2l
TitleCrystal Structure of TEAD2 in a covalent complex with TED-662
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / TEAD / inhibitor / complex / covalent / allosteric / Transcriptional enhancer factor TEF-4
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 / embryonic organ development / vasculogenesis / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / chromatin / 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-EFI / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.O.
Funding support United States, 4items
OrganizationGrant numberCountry
American Cancer SocietyRSG-12-092-01-CDD United States
Other privateVera Bradley Foundation United States
Other governmentIndiana University Simon Cancer Center Near Miss Initiative grant United States
Other private100 Voices of Hope United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Small-Molecule Cyanamide Pan-TEAD·YAP1 Covalent Antagonists.
Authors: Bum-Erdene, K. / Yeh, I.J. / Gonzalez-Gutierrez, G. / Ghozayel, M.K. / Pollok, K. / Meroueh, S.O.
History
DepositionDec 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)53,5643
Polymers53,2542
Non-polymers3091
Water84747
1
B: Transcriptional enhancer factor TEF-4


Theoretical massNumber of molelcules
Total (without water)26,6271
Polymers26,6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9362
Polymers26,6271
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.651, 61.746, 79.753
Angle α, β, γ (deg.)90.000, 117.334, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-524-

HOH

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Components

#1: Protein Transcriptional enhancer factor TEF-4 / TEA domain family member 2 / TEAD-2


Mass: 26627.170 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 BL21(DE3) (bacteria) / References: UniProt: Q15562
#2: Chemical ChemComp-EFI / (3aR,4R,7aS)-4-[3-(trifluoromethyl)anilino]octahydro-2H-isoindole-2-carbonitrile


Mass: 309.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18F3N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium Formate 1.8M - 2.4M HEPES, pH 7.2-7.4 / PH range: 7.2 -7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.15→53.61 Å / Num. obs: 14087 / % possible obs: 87.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 39.71 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.055 / Rrim(I) all: 0.107 / Rsym value: 0.091 / Net I/σ(I): 10.6
Reflection shellResolution: 2.15→2.49 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 704 / CC1/2: 0.485 / Rpim(I) all: 0.579 / Rrim(I) all: 1.088 / Rsym value: 0.916 / % possible all: 62.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E5G

6e5g


Resolution: 2.15→53.61 Å / SU ML: 0.2559 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.7854
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2566 710 5.04 %
Rwork0.2032 13371 -
obs0.2058 14081 48.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.16 Å2
Refinement stepCycle: LAST / Resolution: 2.15→53.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 22 47 3356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563398
X-RAY DIFFRACTIONf_angle_d0.79774594
X-RAY DIFFRACTIONf_chiral_restr0.0503500
X-RAY DIFFRACTIONf_plane_restr0.0062585
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.310.3906100.3496X-RAY DIFFRACTION1.87
2.32-2.550.3858360.341846X-RAY DIFFRACTION15.42
2.55-2.920.32241070.2862331X-RAY DIFFRACTION42.45
2.92-3.670.28692750.22874691X-RAY DIFFRACTION86.2
3.67-53.610.22592820.17325407X-RAY DIFFRACTION96.92
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)
13.72669962180.07493523706650.9099304847241.319135057091.387396949535.30744179167-0.0389340905223-0.3150029324140.0467413120631-0.079264686668-0.0593777350021-0.0486569889964-0.0907946441608-0.4806122272850.08600668219540.2582849682550.03782757146430.009981641179770.09445735605020.03877838010790.16264370021727.1177369543-13.403312655619.3790200205
24.182788330370.626264590194-1.357310547882.67869159042-1.08184023435.24527791187-0.01781683325070.2459097782330.144693798582-0.08701655163760.2264271455280.48734428168-0.2202729115980.126625838387-0.2464116011620.2771495637350.1539539097460.04648507350250.4207356913030.07139220355440.31974961375117.251234980615.096255841719.4818319157
33.480407370541.37356682147-3.944267997271.05748792785-1.227254092547.831736023940.117461101722-0.7257764482760.264486781223-0.01963506326660.06951604352830.1118675102040.1095821595020.818722990746-0.1514264720170.2665609207640.125423642790.01294323146440.1684319818810.02249108698030.27039760942323.92072395913.242373857220.9257097183
45.13389781976-0.8711559314793.290728552193.361003616511.366463265617.73304634834-0.0107424762485-0.357938696952-0.299180777676-0.1338618285930.106976569622-0.4510793457490.2806468137980.316435960628-0.07055036335540.1544256057450.00835128513839-0.0286271707980.02290772521710.03791498381750.086594051129932.7009732588-16.900656079521.6782960892
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 305 through 446 )BA305 - 44685 - 212
22chain 'A' and (resid 222 through 293 )AB222 - 2931 - 55
33chain 'A' and (resid 294 through 446 )AB294 - 44656 - 190
44chain 'B' and (resid 217 through 304 )BA217 - 3041 - 84

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