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- PDB-6jk0: Crystal Structure of YAP1 and Dendrin complex -

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Basic information

Entry
Database: PDB / ID: 6jk0
TitleCrystal Structure of YAP1 and Dendrin complex
ComponentsTranscriptional coactivator YAP1,Dendrin
KeywordsSIGNALING PROTEIN / WW tandem / PY tandem / KIBRA / PTPN14
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 / enterocyte differentiation / regulation of keratinocyte proliferation / intestinal epithelial cell differentiation / glandular epithelial cell differentiation / 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 / enterocyte differentiation / regulation of keratinocyte proliferation / intestinal epithelial cell differentiation / glandular epithelial cell differentiation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / 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 / hippo signaling / regulation of stem cell proliferation / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / tissue homeostasis / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / dendritic spine membrane / regulation of canonical Wnt signaling pathway / organ growth / interleukin-6-mediated signaling pathway / negative regulation of epithelial cell differentiation / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / positive regulation of stem cell population maintenance / blastocyst development / signal transduction in response to DNA damage / somatic stem cell population maintenance / regulation of neurogenesis / bicellular tight junction / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / positive regulation of cardiac muscle cell proliferation / keratinocyte differentiation / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / epithelial cell differentiation / response to progesterone / epithelial cell proliferation / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cellular response to gamma radiation / positive regulation of protein localization to nucleus / cell morphogenesis / cell-cell junction / transcription corepressor activity / positive regulation of canonical Wnt signaling pathway / presynapse / regulation of cell population proliferation / regulation of gene expression / positive regulation of cell growth / protein-containing complex assembly / perikaryon / transcription regulator complex / DNA-binding transcription factor binding / postsynaptic membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / cell population proliferation / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / positive regulation of cell population proliferation / dendrite / chromatin binding / positive regulation of gene expression / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Dendrin / Nephrin and CD2AP-binding protein, Dendrin / : / Omega loop, TEAD interacting region 3 / : / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Transcriptional coactivator YAP1 / Dendrin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLin, Z. / Yang, Z. / Ji, Z. / Zhang, M.
CitationJournal: Elife / Year: 2019
Title: Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.
Authors: Lin, Z. / Yang, Z. / Xie, R. / Ji, Z. / Guan, K. / Zhang, M.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 coactivator YAP1,Dendrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7693
Polymers14,6891
Non-polymers802
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.606, 94.606, 174.397
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Transcriptional coactivator YAP1,Dendrin / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 14689.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: YAP1 (residues 156-247 from Uniprot P46938) linked Dendrin (residues 222-241 from Uniprot Q80TS7)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Yap1, Yap, Yap65, Ddn, Gm748, Kiaa0749 / Production host: Escherichia coli (E. coli) / References: UniProt: P46938, UniProt: Q80TS7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 7.67 Å3/Da / Density % sol: 83.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25-30% w/v PEG400, 200mM CaCl2, 100mM HEPS (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 8993 / % possible obs: 99.9 % / Redundancy: 34.6 % / Rmerge(I) obs: 0.225 / Net I/σ(I): 15.3
Reflection shellResolution: 3.1→3.15 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2 / Num. unique obs: 444 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4REX

4rex


Resolution: 3.1→32.059 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.62
RfactorNum. reflection% reflection
Rfree0.2428 848 10.09 %
Rwork0.2131 --
obs0.216 8406 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→32.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 2 5 886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018911
X-RAY DIFFRACTIONf_angle_d1.2651249
X-RAY DIFFRACTIONf_dihedral_angle_d16.62328
X-RAY DIFFRACTIONf_chiral_restr0.069125
X-RAY DIFFRACTIONf_plane_restr0.006168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0974-3.29120.39621210.33641089X-RAY DIFFRACTION84
3.2912-3.54510.32571370.27731204X-RAY DIFFRACTION93
3.5451-3.90130.25271450.21591274X-RAY DIFFRACTION97
3.9013-4.46450.20141430.18351278X-RAY DIFFRACTION97
4.4645-5.61980.22481480.1781329X-RAY DIFFRACTION98
5.6198-32.06050.21381540.20551384X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 9.2232 Å / Origin y: 49.3012 Å / Origin z: 68.9995 Å
111213212223313233
T0.5504 Å2-0.0207 Å2-0.028 Å2-0.565 Å2-0.0414 Å2--0.5316 Å2
L0.8666 °2-0.5003 °20.6677 °2-0.8026 °20.3712 °2--2.7994 °2
S0.0505 Å °0.028 Å °-0.1549 Å °-0.0074 Å °0.0706 Å °0.0003 Å °-0.0282 Å °0.3168 Å °-0.1051 Å °
Refinement TLS groupSelection details: all

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