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- PDB-7oyj: Crystal structure of hTEAD2 in complex with fragment at the inter... -

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Basic information

Entry
Database: PDB / ID: 7oyj
TitleCrystal structure of hTEAD2 in complex with fragment at the interface 2
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / TEAD / Fragment
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 / 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
3-(1~{H}-pyrazol-5-yl)aniline / PALMITIC ACID / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsGuichou, J.F. / Gelin, M. / Allemand, F.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Toward the Design of Ligands Selective for the C-Terminal Domain of TEADs.
Authors: Liberelle, M. / Toulotte, F. / Renault, N. / Gelin, M. / Allemand, F. / Melnyk, P. / Guichou, J.F. / Cotelle, P.
History
DepositionJun 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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-4
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6505
Polymers54,9782
Non-polymers6723
Water1,08160
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7462
Polymers27,4891
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9053
Polymers27,4891
Non-polymers4162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.507, 61.294, 80.224
Angle α, β, γ (deg.)90.000, 111.220, 90.000
Int Tables number5
Space group name H-MC121
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: 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-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3DI / 3-(1~{H}-pyrazol-5-yl)aniline / 3-(1H-pyrazol-5yl)aniline


Mass: 159.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.8M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.592→74.786 Å / Num. obs: 65881 / % possible obs: 91.8 % / Redundancy: 2.4 % / Biso Wilson estimate: 36.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.025 / Rrim(I) all: 0.042 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.592-1.7942.50.537533921290.7130.3860.6651.665.4
5.091-74.7862.40.025503321280.9950.020.03240.897.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DQ8

5dq8


Resolution: 1.91→53.04 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 3272 4.97 %
Rwork0.1955 62609 -
obs0.1968 65881 83.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.39 Å2 / Biso mean: 53.448 Å2 / Biso min: 27.21 Å2
Refinement stepCycle: final / Resolution: 1.91→53.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 40 60 3330
Biso mean--60.25 51.2 -
Num. residues----396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.930.34171600.31962650281083
1.93-1.960.37781390.28932715285483
1.96-20.3111310.28392671280283
2-2.030.32581140.26632718283281
2.03-2.070.30731160.25472603271980
2.07-2.110.26431460.24292573271980
2.11-2.150.26841530.22142661281481
2.15-2.20.21311300.21112725285585
2.2-2.250.21591720.21062817298986
2.25-2.310.21631410.20672813295487
2.31-2.370.26851560.2092711286785
2.37-2.440.26191450.21522780292586
2.44-2.520.28381540.2132785293985
2.52-2.610.26041230.20812740286385
2.61-2.710.23561580.21582745290384
2.71-2.830.23561390.21972694283383
2.83-2.980.2811280.21552550267878
2.98-3.170.26211610.20632649281082
3.17-3.410.16711530.18772813296686
3.42-3.760.22721480.17252808295686
3.76-4.30.16881340.16592789292385
4.3-5.420.21591370.15222747288484
5.42-53.040.17651340.20912852298688
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)
15.54170.5963-0.97663.2518-1.02624.9378-0.04040.0786-0.0511-0.05670.22180.2482-0.0579-0.0351-0.18280.45370.04240.06310.224600.2953-36.590720.533420.6434
22.04360.3043-1.56911.5197-0.7475.95390.0845-0.24550.0504-0.05610.08930.14140.16730.4311-0.14720.36050.06040.02250.26390.01660.3104-32.48116.861622.0963
34.196-0.18741.51023.09060.5064.8975-0.1703-0.2458-0.2961-0.00610.184-0.32390.17870.2847-0.0020.3240.02840.00250.3101-0.02450.2558-27.5315-13.910123.3955
42.34260.21760.31941.79591.36274.7001-0.0335-0.17950.0657-0.15890.099-0.1658-0.1603-0.1622-0.07410.31050.05140.02030.21910.0120.301-28.8639-9.551719.9691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 221 through 325 )A221 - 325
2X-RAY DIFFRACTION2chain 'A' and (resid 326 through 447 )A326 - 447
3X-RAY DIFFRACTION3chain 'B' and (resid 220 through 293 )B220 - 293
4X-RAY DIFFRACTION4chain 'B' and (resid 294 through 446 )B294 - 446

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