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- PDB-4ln0: Crystal structure of the VGLL4-TEAD4 complex -

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Basic information

Entry
Database: PDB / ID: 4ln0
TitleCrystal structure of the VGLL4-TEAD4 complex
Components
  • Transcription cofactor vestigial-like protein 4
  • Transcriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION / TEA/ATTS domain family / Vestigial/Tondu family / Transcription factor / Transcription cofactor / Development
Function / homology
Function and homology information


RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell fate commitment / negative regulation of cardiac muscle cell proliferation / hippo signaling / blastocyst formation / cell fate specification / positive regulation of stem cell population maintenance / negative regulation of hippo signaling / negative regulation of Wnt signaling pathway ...RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell fate commitment / negative regulation of cardiac muscle cell proliferation / hippo signaling / blastocyst formation / cell fate specification / positive regulation of stem cell population maintenance / negative regulation of hippo signaling / negative regulation of Wnt signaling pathway / cell fate commitment / embryonic organ development / embryo implantation / protein-DNA complex / negative regulation of cell growth / transcription coactivator binding / positive regulation of protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription cofactor vestigial-like protein 4 / Transcription cofactor vestigial-like protein 4 / TDU repeat / Short repeats in human TONDU, fly vestigial and other proteins. / 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 ...Transcription cofactor vestigial-like protein 4 / Transcription cofactor vestigial-like protein 4 / TDU repeat / Short repeats in human TONDU, fly vestigial and other proteins. / 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 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Transcriptional enhancer factor TEF-3 / Transcription cofactor vestigial-like protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.896 Å
AuthorsWang, H. / Shi, Z. / Zhou, Z.
CitationJournal: Cancer Cell / Year: 2014
Title: A Peptide Mimicking VGLL4 Function Acts as a YAP Antagonist Therapy against Gastric Cancer.
Authors: Jiao, S. / Wang, H. / Shi, Z. / Dong, A. / Zhang, W. / Song, X. / He, F. / Wang, Y. / Zhang, Z. / Wang, W. / Wang, X. / Guo, T. / Li, P. / Zhao, Y. / Ji, H. / Zhang, L. / Zhou, Z.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-3
B: Transcriptional enhancer factor TEF-3
C: Transcription cofactor vestigial-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6788
Polymers58,1763
Non-polymers5035
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-15 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.817, 94.817, 135.172
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Transcriptional enhancer factor TEF-3 / ETF-related factor 2 / ETFR-2 / TEA domain family member 4 / TEAD-4 / TEF-1-related factor 1 / TEF- ...ETF-related factor 2 / ETFR-2 / TEA domain family member 4 / TEAD-4 / TEF-1-related factor 1 / TEF-1-related factor FR-19 / RTEF-1


Mass: 25933.324 Da / Num. of mol.: 2 / Fragment: YAP binding domain, UNP RESIDUES 209-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tcf13r1, Tead4, Tef3, Tefr1 / Plasmid: plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62296
#2: Protein Transcription cofactor vestigial-like protein 4 / Vgl-4


Mass: 6308.972 Da / Num. of mol.: 1 / Fragment: Tondu domain, UNP RESIDUES 203-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vgll4 / Plasmid: plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q80V24
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.02 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M L-proline, 0.1M HEPES pH 7.5, 24% PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.896→50 Å / Num. all: 16149 / Num. obs: 15590 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 43.21 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 15.86
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 5.28 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JUA

3jua


Resolution: 2.896→41.057 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 1552 9.96 %RANDOM
Rwork0.1855 ---
all0.1918 16148 --
obs0.1918 15584 96.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.896→41.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 0 33 7 3695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093789
X-RAY DIFFRACTIONf_angle_d1.2615119
X-RAY DIFFRACTIONf_dihedral_angle_d16.6381347
X-RAY DIFFRACTIONf_chiral_restr0.052560
X-RAY DIFFRACTIONf_plane_restr0.006640
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8962-2.98960.33591400.2449125898
2.9896-3.09640.34811390.2421127798
3.0964-3.22040.29311420.2229126497
3.2204-3.36690.26551370.203127698
3.3669-3.54430.22651380.1911125197
3.5443-3.76620.26861390.167128397
3.7662-4.05670.22721440.1683126197
4.0567-4.46450.1871450.1509127996
4.4645-5.10950.21751400.1388127096
5.1095-6.43350.22881370.1958128595
6.4335-41.06130.26141510.2086132894

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