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- PDB-5gzb: Crystal Structure of Transcription Factor TEAD4 in Complex with M... -

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Basic information

Entry
Database: PDB / ID: 5gzb
TitleCrystal Structure of Transcription Factor TEAD4 in Complex with M-CAT DNA
Components
  • DNA (5'-D(*GP*AP*GP*AP*GP*GP*AP*AP*TP*GP*CP*AP*A)-3')
  • DNA (5'-D(*TP*TP*GP*CP*AP*TP*TP*CP*CP*TP*CP*TP*C)-3')
  • Transcriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION/DNA / Transcription factor / DNA / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


trophectodermal cell fate commitment / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / Formation of axial mesoderm / cell fate specification / muscle organ development / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / embryonic organ development ...trophectodermal cell fate commitment / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / Formation of axial mesoderm / cell fate specification / muscle organ development / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / embryonic organ development / embryo implantation / skeletal system development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcriptional enhancer factor TEF-3 (TEAD4) / 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
PHOSPHATE ION / DNA / DNA (> 10) / Transcriptional enhancer factor TEF-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.704 Å
AuthorsHe, F. / Shi, Z.B. / Zhou, Z.C.
CitationJournal: Oncogene / Year: 2017
Title: DNA-binding mechanism of the Hippo pathway transcription factor TEAD4
Authors: Shi, Z.B. / He, F. / Chen, M. / Hua, L. / Wang, W. / Jiao, S. / Zhou, Z.C.
History
DepositionSep 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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: DNA (5'-D(*TP*TP*GP*CP*AP*TP*TP*CP*CP*TP*CP*TP*C)-3')
C: DNA (5'-D(*GP*AP*GP*AP*GP*GP*AP*AP*TP*GP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4165
Polymers20,2293
Non-polymers1872
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-27 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.595, 118.595, 110.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transcriptional enhancer factor TEF-3 / TEA domain family member 4 / TEAD-4 / Transcription factor 13-like 1 / Transcription factor RTEF-1


Mass: 12286.553 Da / Num. of mol.: 1 / Fragment: UNP residues 36-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15561

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*TP*TP*GP*CP*AP*TP*TP*CP*CP*TP*CP*TP*C)-3') / M-CAT element


Mass: 3868.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*AP*GP*AP*GP*GP*AP*AP*TP*GP*CP*AP*A)-3') / M-CAT element


Mass: 4073.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.79 Å3/Da / Density % sol: 74.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.6 M Na2HPO4, 0.6 M KH2PO4, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 30, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.7→37.5 Å / Num. obs: 20397 / % possible obs: 99.7 % / Redundancy: 9.3 % / Net I/σ(I): 20.3
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.725 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.704→37.5 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.78
RfactorNum. reflection% reflection
Rfree0.2562 2034 9.97 %
Rwork0.2291 --
obs0.2318 20397 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 81.19 Å2
Refinement stepCycle: LAST / Resolution: 2.704→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms701 525 11 1 1238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041307
X-RAY DIFFRACTIONf_angle_d0.6361868
X-RAY DIFFRACTIONf_dihedral_angle_d25.344527
X-RAY DIFFRACTIONf_chiral_restr0.027208
X-RAY DIFFRACTIONf_plane_restr0.002148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7041-2.7670.46711250.40571206X-RAY DIFFRACTION98
2.767-2.83620.49491320.40471235X-RAY DIFFRACTION100
2.8362-2.91290.41441230.39631239X-RAY DIFFRACTION99
2.9129-2.99850.42471470.3681215X-RAY DIFFRACTION100
2.9985-3.09530.40441340.3151229X-RAY DIFFRACTION100
3.0953-3.20590.34211410.27551220X-RAY DIFFRACTION98
3.2059-3.33410.25981310.23651209X-RAY DIFFRACTION99
3.3341-3.48580.24431410.24791210X-RAY DIFFRACTION98
3.4858-3.66940.28581360.26731219X-RAY DIFFRACTION99
3.6694-3.89910.2951400.23051231X-RAY DIFFRACTION100
3.8991-4.19980.25251450.21041219X-RAY DIFFRACTION100
4.1998-4.62170.18291380.19391242X-RAY DIFFRACTION100
4.6217-5.28890.24211280.20461248X-RAY DIFFRACTION100
5.2889-6.65740.21431430.20641220X-RAY DIFFRACTION100
6.6574-37.50660.18651300.17141221X-RAY DIFFRACTION98

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