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- PDB-6vah: Crystal structure of human TEAD2 transcription factor in complex ... -

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Basic information

Entry
Database: PDB / ID: 6vah
TitleCrystal structure of human TEAD2 transcription factor in complex with Flufenamic acid derivative
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / TEAD2 / transcription factor / Structural Genomics / Structural Genomics Consortium / SGC
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 / 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
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
2-fluoro-6-[(3-hexylphenyl)amino]benzoic acid / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.11 Å
AuthorsHalabelian, L. / Zeng, H. / Dong, A. / Li, Y. / Melin, L. / Gagnon, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Santhakumar, V. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of human TEAD2 transcription factor in complex with Flufenamic acid derivative
Authors: Halabelian, L. / Zeng, H. / Dong, A. / Li, Y. / Melin, L. / Gagnon, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Santhakumar, V. / Structural Genomics Consortium (SGC)
History
DepositionDec 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)55,6095
Polymers54,9782
Non-polymers6313
Water50428
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8042
Polymers27,4891
Non-polymers3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8043
Polymers27,4891
Non-polymers3152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.792, 61.307, 79.862
Angle α, β, γ (deg.)90.000, 118.100, 90.000
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 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pRARE2 / References: UniProt: Q15562
#2: Chemical ChemComp-QZ1 / 2-fluoro-6-[(3-hexylphenyl)amino]benzoic acid


Mass: 315.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22FNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 48.15 % / Mosaicity: 0.71 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5M Na Formate, and 0.1M Bis-Tris Propane pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28671 / % possible obs: 97 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.048 / Rrim(I) all: 0.105 / Χ2: 1.531 / Net I/σ(I): 9.2 / Num. measured all: 117595
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.90.55112820.8470.3260.6450.65888.2
2.14-2.1830.50313750.8990.2870.5830.6993.1
2.18-2.223.20.52613800.8130.3010.6110.68594.8
2.22-2.263.40.51214210.8490.2830.5880.68996.5
2.26-2.313.40.50113940.8780.2770.5760.70795.7
2.31-2.373.50.47313700.9150.2580.5420.69994.2
2.37-2.424.20.48814630.9390.2490.5510.6598.9
2.42-2.494.60.45414930.960.2260.5090.6999.9
2.49-2.564.80.39714690.9690.1940.4430.72599.9
2.56-2.654.80.32514670.9710.160.3640.75999.8
2.65-2.744.70.27214520.9770.1340.3040.83899.2
2.74-2.854.70.21114570.9840.1050.2360.92899
2.85-2.984.60.1714470.9870.0850.191.10599.3
2.98-3.144.40.12714740.9920.0650.1431.3799
3.14-3.334.10.09714400.9940.0510.111.9396.4
3.33-3.594.10.07814200.9940.040.0882.4996
3.59-3.954.60.06614810.9950.0340.0753.08699.6
3.95-4.524.30.05614580.9960.030.0643.40598
4.52-5.74.10.05214610.9960.0270.0593.66496.9
5.7-5040.0514670.9960.0270.0573.77295.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5DQ8

5dq8


Resolution: 2.11→39.07 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.636 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.182
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 1415 4.9 %RANDOM
Rwork0.2035 ---
obs0.2055 27256 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 129.32 Å2 / Biso mean: 50.628 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å2-0 Å22.02 Å2
2---0.98 Å2-0 Å2
3----3.63 Å2
Refinement stepCycle: final / Resolution: 2.11→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 47 28 3208
Biso mean--54.59 50.31 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133290
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172932
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.644468
X-RAY DIFFRACTIONr_angle_other_deg1.2091.5816728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.465404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14121.646158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50515483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9421521
X-RAY DIFFRACTIONr_chiral_restr0.0560.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02755
LS refinement shellResolution: 2.111→2.166 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 80 -
Rwork0.287 1672 -
all-1752 -
obs--81.56 %

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