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- PDB-3jua: Structural basis of YAP recognition by TEAD4 in the Hippo pathway -

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Basic information

Entry
Database: PDB / ID: 3jua
TitleStructural basis of YAP recognition by TEAD4 in the Hippo pathway
Components
  • 65 kDa Yes-associated protein
  • Transcriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION / TEAD / YAP / Hippo pathway / Activator / DNA-binding / Nucleus / Transcription regulation / Phosphoprotein
Function / homology
Function and homology information


Nuclear signaling by ERBB4 / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Signaling by Hippo / trophectodermal cell fate commitment / intestinal epithelial cell differentiation / enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration ...Nuclear signaling by ERBB4 / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Signaling by Hippo / trophectodermal cell fate commitment / intestinal epithelial cell differentiation / enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / bud elongation involved in lung branching / RUNX1 regulates transcription of genes involved in differentiation of HSCs / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / heart process / positive regulation of organ growth / trophectodermal cell differentiation / paraxial mesoderm development / regulation of stem cell proliferation / hippo signaling / tissue homeostasis / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / negative regulation of stem cell differentiation / blastocyst formation / embryonic heart tube morphogenesis / female germ cell nucleus / regulation of canonical Wnt signaling pathway / proline-rich region binding / cell fate specification / negative regulation of epithelial cell differentiation / organ growth / interleukin-6-mediated signaling pathway / positive regulation of stem cell population maintenance / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / somatic stem cell population maintenance / blastocyst development / regulation of neurogenesis / signal transduction in response to DNA damage / canonical Wnt signaling pathway / cell fate commitment / vasculogenesis / embryonic organ development / positive regulation of osteoblast differentiation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / embryo implantation / epithelial cell proliferation / positive regulation of epithelial cell proliferation / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / protein-DNA complex / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / cell-cell junction / positive regulation of canonical Wnt signaling pathway / regulation of cell population proliferation / positive regulation of cell growth / regulation of gene expression / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / in utero embryonic development / cell population proliferation / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / transcription cis-regulatory region 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 gene expression / DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
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
Transcriptional coactivator YAP1 / Transcriptional enhancer factor TEF-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsChen, L. / Song, H.
CitationJournal: Genes Dev. / Year: 2010
Title: Structural basis of YAP recognition by TEAD4 in the hippo pathway.
Authors: Chen, L. / Chan, S.W. / Zhang, X. / Walsh, M. / Lim, C.J. / Hong, W. / Song, H.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: 65 kDa Yes-associated protein
C: Transcriptional enhancer factor TEF-3
D: 65 kDa Yes-associated protein
E: Transcriptional enhancer factor TEF-3
F: 65 kDa Yes-associated protein
G: Transcriptional enhancer factor TEF-3
H: 65 kDa Yes-associated protein


Theoretical massNumber of molelcules
Total (without water)120,8938
Polymers120,8938
Non-polymers00
Water3,585199
1
A: Transcriptional enhancer factor TEF-3
B: 65 kDa Yes-associated protein


Theoretical massNumber of molelcules
Total (without water)30,2232
Polymers30,2232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-16 kcal/mol
Surface area12830 Å2
MethodPISA
2
C: Transcriptional enhancer factor TEF-3
D: 65 kDa Yes-associated protein


Theoretical massNumber of molelcules
Total (without water)30,2232
Polymers30,2232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-18 kcal/mol
Surface area13300 Å2
MethodPISA
3
E: Transcriptional enhancer factor TEF-3
F: 65 kDa Yes-associated protein


Theoretical massNumber of molelcules
Total (without water)30,2232
Polymers30,2232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-19 kcal/mol
Surface area13410 Å2
MethodPISA
4
G: Transcriptional enhancer factor TEF-3
H: 65 kDa Yes-associated protein


Theoretical massNumber of molelcules
Total (without water)30,2232
Polymers30,2232
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-2 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.982, 146.910, 165.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21G
12C
22E
13B
23H
14D
24F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A173 - 185
2116G173 - 185
1216A194 - 200
2216G194 - 200
1316A215 - 237
2316G215 - 237
1416A240 - 250
2416G240 - 250
1516A275 - 295
2516G275 - 295
1616A306 - 352
2616G306 - 352
1716A355 - 370
2716G355 - 370
1816A375 - 382
2816G375 - 382
1126C173 - 185
2126E173 - 185
1226C194 - 200
2226E194 - 200
1326C215 - 237
2326E215 - 237
1426C240 - 250
2426E240 - 250
1526C275 - 295
2526E275 - 295
1626C306 - 352
2626E306 - 352
1726C355 - 370
2726E355 - 370
1826C375 - 382
2826E375 - 382
1136B47 - 83
2136H47 - 83
1146D48 - 83
2146F48 - 83

NCS ensembles :
ID
1
2
3
4

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Components

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


Mass: 25775.168 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, Tef3, Tefr1 / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / References: UniProt: Q62296
#2: Protein/peptide
65 kDa Yes-associated protein / YAP65


Mass: 4448.143 Da / Num. of mol.: 4 / Fragment: UNP residues 47-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Yap, Yap1, Yap65 / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / References: UniProt: P46938
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 5.076 Å3/Da / Density % sol: 75.77 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 5.6
Details: PEG10000, Mg Acetate, pH5.6, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Nov 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→74.346 Å / Num. obs: 61276 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.8-2.93.60.6051.22113959280.605100
2.9-3.013.60.4511.72068457420.451100
3.01-3.133.70.3042.52024155400.304100
3.13-3.273.70.2123.61953053070.212100
3.27-3.433.70.1375.41875650720.137100
3.43-3.613.70.14.41796748640.1100
3.61-3.833.70.07101690345880.07100
3.83-4.13.70.05213.11585943140.052100
4.1-4.433.70.043151484740550.043100
4.43-4.853.70.03418.11361237270.03499.9
4.85-5.423.60.03119.81230733900.03199.9
5.42-6.263.60.03518.21082430080.03599.9
6.26-7.673.50.0320.9908825740.0399.9
7.67-10.843.40.02519686620140.02599.8
10.84-74.353.10.03114.9353511530.03197.8

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.4.0077refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: SAD / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.867 / Occupancy max: 1 / Occupancy min: 1 / SU B: 35.092 / SU ML: 0.291 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.529 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28842 2516 5.1 %RANDOM
Rwork0.23633 ---
obs0.23893 47233 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.22 Å2 / Biso mean: 28.077 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å2-0 Å2-0 Å2
2--2.52 Å20 Å2
3----4.34 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7856 0 0 199 8055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228053
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.95310876
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2715934
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26123.925400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.748151423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8031544
X-RAY DIFFRACTIONr_chiral_restr0.1110.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216093
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4671.54767
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89827754
X-RAY DIFFRACTIONr_scbond_it1.12733286
X-RAY DIFFRACTIONr_scangle_it1.9514.53122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A923LOOSE POSITIONAL0.665
1A923LOOSE THERMAL2.3110
2C1020LOOSE POSITIONAL0.795
2C1020LOOSE THERMAL1.4510
3B158LOOSE POSITIONAL1.135
3B158LOOSE THERMAL2.810
4D279LOOSE POSITIONAL1.145
4D279LOOSE THERMAL2.3710
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 179 -
Rwork0.35 3410 -
all-3589 -
obs--99.97 %
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)
12.272-1.9101-1.37213.95461.09551.5195-0.04540.1127-0.08420.2448-0.00130.03590.18150.02840.04670.4035-0.0036-0.08910.33020.06660.3166-11.411-43.11211.752
28.67310.3711.04045.0295-0.28968.8870.00660.9809-0.147-0.6452-0.11180.1190.33440.40360.10520.50510.1405-0.03250.2853-0.020.5643-0.61-52.6380.379
30.46490.1038-0.15233.20881.39233.99230.022-0.08390.1672-0.2860.0498-0.0306-0.3488-0.0881-0.07180.3838-0.03070.03320.3606-0.04630.0293-22.49-1.01235.044
43.8294-1.0675-0.25747.96490.53276.49620.17340.10570.6415-0.12440.01660.4156-0.3931-0.6503-0.19010.5258-0.03720.0010.3267-0.01540.0298-25.8168.04752.31
51.2963-0.31690.79643.0662-0.90363.8737-0.0390.04840.27080.16420.15130.0507-0.47280.0079-0.11230.4152-0.03030.03950.31570.00540.0117-28.198-2.629-1.252
65.15560.3442-1.15568.9404-0.49667.197-0.02410.02411.1616-0.04930.2235-0.3718-0.78440.8339-0.19940.72890.0198-0.02010.52610.0830.0138-27.0647.312-18.671
72.82911.4165-0.49022.1899-0.20251.2826-0.0756-0.6874-0.18670.1639-0.00850.14190.3136-0.23890.08410.7235-0.07090.05240.741-0.04180.467-42.758-42.59227.799
88.035-3.4967-2.63338.05692.26236.15140.1768-0.42580.19070.27340.113-0.06820.5662-0.5821-0.28990.7949-0.15680.12110.8891-0.02360.8307-60.011-50.66331.021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A208 - 426
2X-RAY DIFFRACTION2B47 - 84
3X-RAY DIFFRACTION3C208 - 426
4X-RAY DIFFRACTION4D48 - 81
5X-RAY DIFFRACTION5E202 - 426
6X-RAY DIFFRACTION6F48 - 82
7X-RAY DIFFRACTION7G207 - 426
8X-RAY DIFFRACTION8H65 - 82

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