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- PDB-7t2m: Crystal Structure of TEAD2 in a covalent complex with TED-664 -

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Basic information

Entry
Database: PDB / ID: 7t2m
TitleCrystal Structure of TEAD2 in a covalent complex with TED-664
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-EGK / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 23, 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
Water00
1
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9362
Polymers26,6271
Non-polymers3091
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcriptional enhancer factor TEF-4


Theoretical massNumber of molelcules
Total (without water)26,6271
Polymers26,6271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.106, 61.570, 79.511
Angle α, β, γ (deg.)90.000, 112.685, 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

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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-EGK / (3aR,4R,7aS)-4-[2-(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
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: 2.36 Å3/Da / Density % sol: 47.79 %
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: 1.07216 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07216 Å / Relative weight: 1
ReflectionResolution: 2.81→52.78 Å / Num. obs: 7956 / % possible obs: 89.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 55.57 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.084 / Rrim(I) all: 0.163 / Rsym value: 0.139 / Net I/σ(I): 5.7
Reflection shellResolution: 2.81→3.11 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 398 / CC1/2: 0.501 / Rpim(I) all: 0.56 / Rrim(I) all: 1.077 / Rsym value: 0.916 / % possible all: 59.8

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Processing

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

6e5g


Resolution: 2.81→52.78 Å / SU ML: 0.3642 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.9943
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2789 388 4.88 %
Rwork0.2213 7564 -
obs0.2242 7952 64.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.79 Å2
Refinement stepCycle: LAST / Resolution: 2.81→52.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 22 0 3308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00973387
X-RAY DIFFRACTIONf_angle_d1.06664572
X-RAY DIFFRACTIONf_chiral_restr0.0543494
X-RAY DIFFRACTIONf_plane_restr0.0084582
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-3.220.31290.3141667X-RAY DIFFRACTION17.2
3.22-4.050.31731280.23743012X-RAY DIFFRACTION77.59
4.06-52.780.26242310.2073885X-RAY DIFFRACTION99.37
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)
10.144472291032-0.317393221445-0.01186899190970.9357126136140.07921873453840.956007246844-0.055448344053-0.0148001551114-0.190995551977-0.0747229251716-0.027922206318-0.2113467880350.0895096644987-0.0879954913461-3.02964803348E-90.257647371044-0.05758573634840.003223707249440.233710956969-0.02497221869230.230757217669-26.1541445657-15.531118786619.5134383337
20.4212986281490.3647571383650.243240316746-0.09629649254160.342917386133-0.0441444505528-0.629345466286-0.3045100713550.0483534385539-0.539855128064-0.331547443232-0.7274661699590.94527153459-0.272501978809-1.49380388533E-70.1723464012090.0256167128559-0.04471828945450.480186268833-0.07753101349960.191496775975-30.6321070641-8.2904076228327.2335043042
30.6465502936080.107926846390.2056641775290.151295845693-0.5670360145550.575321943678-0.0486626773496-0.0242258520997-0.101880904725-0.1059709501520.0772254354075-0.1373332354210.125930006374-0.08588047630294.97249298328E-90.2355803974510.056526863823-0.002656077194890.140490853125-0.02540794098220.195890274717-27.7753096491-14.804431672613.4708741946
4-0.01093676335250.378467496383-0.09040738617410.598619159580.1052544457650.8041239847850.3803852935410.3335883413680.6151864872270.169441233958-0.007638453904450.134431556739-0.455938119214-0.1581369264525.77901156132E-90.3379171225210.05768250476920.02289408139220.4828313249770.0003744647871160.411647653343-38.036173039216.633685224421.4381850288
50.2981028849780.2679214503780.4649932385850.1040650638030.381621637841.221762865830.0305787058026-0.2310186617920.230083471203-0.09826307837220.1472554387350.1636347327270.05549154453640.173598990142-5.7641400222E-90.2847012085270.07752121179820.01678014192810.25893305963-0.03134719322760.291729760079-31.248365554114.131115410321.7602897934
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 222 through 325 )BA222 - 3251 - 82
22chain 'B' and (resid 326 through 380 )BA326 - 38083 - 137
33chain 'B' and (resid 381 through 446 )BA381 - 446138 - 203
44chain 'A' and (resid 222 through 296 )AC222 - 2961 - 61
55chain 'A' and (resid 297 through 446 )AC297 - 44662 - 196

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