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- PDB-5gn0: Structure of TAZ-TEAD complex -

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Basic information

Entry
Database: PDB / ID: 5gn0
TitleStructure of TAZ-TEAD complex
Components
  • Transcriptional enhancer factor TEF-3
  • WW domain-containing transcription regulator protein 1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of SMAD protein signal transduction / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / kidney morphogenesis / Signaling by Hippo / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / trophectodermal cell fate commitment / regulation of metanephric nephron tubule epithelial cell differentiation / mesenchymal cell differentiation / heart process ...regulation of SMAD protein signal transduction / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / kidney morphogenesis / Signaling by Hippo / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / trophectodermal cell fate commitment / regulation of metanephric nephron tubule epithelial cell differentiation / mesenchymal cell differentiation / heart process / stem cell division / hippo signaling / tissue homeostasis / glomerulus development / blastocyst formation / regulation of canonical Wnt signaling pathway / cell fate specification / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / positive regulation of stem cell population maintenance / negative regulation of fat cell differentiation / cilium assembly / cell fate commitment / embryonic organ development / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / embryo implantation / negative regulation of protein phosphorylation / protein-DNA complex / negative regulation of protein kinase activity / negative regulation of canonical Wnt signaling pathway / multicellular organism growth / positive regulation of protein localization to nucleus / osteoblast differentiation / transcription corepressor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Transcriptional enhancer factor TEF-3 (TEAD4) / 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 ...Transcriptional enhancer factor TEF-3 (TEAD4) / 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 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / PALMITIC ACID / Transcriptional enhancer factor TEF-3 / WW domain-containing transcription regulator protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKaan, H.Y.K. / Song, H.
CitationJournal: Sci Rep / Year: 2017
Title: Crystal structure of TAZ-TEAD complex reveals a distinct interaction mode from that of YAP-TEAD complex
Authors: Kaan, H.Y.K. / Chan, S.W. / Tan, S.K.J. / Guo, F. / Lim, C.J. / Hong, W. / Song, H.
History
DepositionJul 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-3
B: Transcriptional enhancer factor TEF-3
C: Transcriptional enhancer factor TEF-3
D: Transcriptional enhancer factor TEF-3
E: WW domain-containing transcription regulator protein 1
F: WW domain-containing transcription regulator protein 1
G: WW domain-containing transcription regulator protein 1
H: WW domain-containing transcription regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,15213
Polymers121,9988
Non-polymers1,1545
Water34219
1
A: Transcriptional enhancer factor TEF-3
E: WW domain-containing transcription regulator protein 1


Theoretical massNumber of molelcules
Total (without water)30,5002
Polymers30,5002
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-3
G: WW domain-containing transcription regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9484
Polymers30,5002
Non-polymers4492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional enhancer factor TEF-3
F: WW domain-containing transcription regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9484
Polymers30,5002
Non-polymers4492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcriptional enhancer factor TEF-3
H: WW domain-containing transcription regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7563
Polymers30,5002
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.660, 120.900, 196.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Transcriptional enhancer factor TEF-3 / TEAD


Mass: 26416.885 Da / Num. of mol.: 4 / Fragment: UNP residues 210-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: TEAD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62296
#2: Protein/peptide
WW domain-containing transcription regulator protein 1 / TAZ


Mass: 4082.652 Da / Num. of mol.: 4 / Fragment: UNP residues 24-57
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Taz / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EPK5
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 6% Polyethylene glycol 10000, 0.05M magnesium acetate, 0.1M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 42312 / % possible obs: 98.6 % / Redundancy: 6.2 % / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JUA

3jua


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.882 / SU B: 16.507 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 0.645 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26013 2131 5 %RANDOM
Rwork0.2004 ---
obs0.2034 40124 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.28 Å2
Baniso -1Baniso -2Baniso -3
1--4.32 Å20 Å20 Å2
2---8.82 Å20 Å2
3---13.14 Å2
Refinement stepCycle: 1 / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8130 0 80 19 8229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198479
X-RAY DIFFRACTIONr_bond_other_d0.0020.027741
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.94711497
X-RAY DIFFRACTIONr_angle_other_deg1.02317787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.39951008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97323.741401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.25151337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0311539
X-RAY DIFFRACTIONr_chiral_restr0.0950.21236
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219543
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022074
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8095.2084056
X-RAY DIFFRACTIONr_mcbond_other3.8085.2074055
X-RAY DIFFRACTIONr_mcangle_it6.1557.8015056
X-RAY DIFFRACTIONr_mcangle_other6.1547.8025057
X-RAY DIFFRACTIONr_scbond_it3.8555.5284423
X-RAY DIFFRACTIONr_scbond_other3.8555.5284424
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3768.1616442
X-RAY DIFFRACTIONr_long_range_B_refined11.51295.05931368
X-RAY DIFFRACTIONr_long_range_B_other11.51295.05831369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 145 -
Rwork0.342 2790 -
obs--93.86 %

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