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- PDB-6cdy: Crystal structure of TEAD complexed with its inhibitor -

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Basic information

Entry
Database: PDB / ID: 6cdy
TitleCrystal structure of TEAD complexed with its inhibitor
ComponentsTranscriptional enhancer factor TEF-4
Keywordstranscription/transcription inhibitor / 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 / Formation of axial mesoderm / regulation of stem cell differentiation / 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 / Formation of axial mesoderm / regulation of stem cell differentiation / embryonic heart tube morphogenesis / embryonic organ development / vasculogenesis / cellular response to retinoic acid / neural tube closure / transcription coactivator binding / sequence-specific double-stranded DNA binding / disordered domain specific 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 / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 1 - #80 / 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 / : ...Coagulation Factor XIII; Chain A, domain 1 - #80 / 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 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-EY1 / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsLIU, S. / HAN, X. / LUO, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK107651 United States
CitationJournal: Cell Stem Cell / Year: 2020
Title: Lats1/2 Sustain Intestinal Stem Cells and Wnt Activation through TEAD-Dependent and Independent Transcription.
Authors: Li, Q. / Sun, Y. / Jarugumilli, G.K. / Liu, S. / Dang, K. / Cotton, J.L. / Xiol, J. / Chan, P.Y. / DeRan, M. / Ma, L. / Li, R. / Zhu, L.J. / Li, J.H. / Leiter, A.B. / Ip, Y.T. / Camargo, F.D. ...Authors: Li, Q. / Sun, Y. / Jarugumilli, G.K. / Liu, S. / Dang, K. / Cotton, J.L. / Xiol, J. / Chan, P.Y. / DeRan, M. / Ma, L. / Li, R. / Zhu, L.J. / Li, J.H. / Leiter, A.B. / Ip, Y.T. / Camargo, F.D. / Luo, X. / Johnson, R.L. / Wu, X. / Mao, J.
History
DepositionFeb 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

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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)55,7154
Polymers54,9782
Non-polymers7372
Water1,18966
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8582
Polymers27,4891
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8582
Polymers27,4891
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.464, 61.640, 80.421
Angle α, β, γ (deg.)90.00, 117.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-601-

HOH

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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-EY1 / 2-[(4H-1,2,4-triazol-3-yl)sulfanyl]-N-{4-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]phenyl}acetamide


Mass: 368.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N4OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.32→40 Å / Num. obs: 22798 / % possible obs: 98.3 % / Redundancy: 4.1 % / Net I/σ(I): 21.1
Reflection shellResolution: 2.32→2.36 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L15

3l15


Resolution: 2.32→38.851 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 26.83
RfactorNum. reflection% reflectionSelection details
Rfree0.255 981 5 %1
Rwork0.1978 ---
obs0.2005 19627 84.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.32→38.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 52 66 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033429
X-RAY DIFFRACTIONf_angle_d0.7874634
X-RAY DIFFRACTIONf_dihedral_angle_d14.8631262
X-RAY DIFFRACTIONf_chiral_restr0.029498
X-RAY DIFFRACTIONf_plane_restr0.004589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3201-2.44240.3189890.21891695X-RAY DIFFRACTION54
2.4424-2.59540.26831110.23722119X-RAY DIFFRACTION68
2.5954-2.79580.30631360.24282580X-RAY DIFFRACTION83
2.7958-3.0770.30691630.23913086X-RAY DIFFRACTION98
3.077-3.5220.27791650.20473131X-RAY DIFFRACTION100
3.522-4.43630.24261470.18592810X-RAY DIFFRACTION89
4.4363-38.85650.20621700.16343225X-RAY DIFFRACTION100
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)
14.8504-0.5359-2.39523.3945-0.9334.8043-0.06720.3951-0.1377-0.16360.2180.5593-0.3209-0.355-0.12270.24140.06270.02630.26490.00760.2335-43.006518.571919.6804
23.12990.2544-2.330.4784-0.39645.01830.0771-0.4690.22580.0460.06740.1956-0.12960.406-0.06850.28240.0647-0.00360.11210.03180.2548-37.240517.031121.0885
34.53160.80031.53611.6250.39573.91310.01030.30760.0635-0.1414-0.1134-0.22610.51310.28620.08970.23040.0365-0.01150.2186-0.00250.1687-29.5126-11.96521.5064
42.70180.22660.59690.66630.81644.9563-0.0217-0.19980.05-0.2156-0.0671-0.11750.0447-0.1960.04450.22310.0456-0.00630.04320.03850.2038-32.8375-9.915519.6773
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 220 through 293 )
4X-RAY DIFFRACTION4chain 'B' and (resid 294 through 447 )

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