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- PDB-6jk1: Crystal Structure of YAP1 and Dendrin complex 2 -

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Basic information

Entry
Database: PDB / ID: 6jk1
TitleCrystal Structure of YAP1 and Dendrin complex 2
ComponentsDendrin,Transcriptional coactivator YAP1
KeywordsSIGNALING PROTEIN / WW tandem / PY tandem / YAP1 / Dendrin
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 / bud elongation involved in lung branching / intestinal 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 / bud elongation involved in lung branching / intestinal epithelial cell differentiation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / glandular epithelial cell differentiation / 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 / tissue homeostasis / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / negative regulation of stem cell differentiation / female germ cell nucleus / embryonic heart tube morphogenesis / dendritic spine membrane / proline-rich region binding / regulation of canonical Wnt signaling pathway / organ growth / negative regulation of epithelial cell differentiation / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / positive regulation of stem cell population maintenance / somatic stem cell population maintenance / blastocyst development / regulation of neurogenesis / signal transduction in response to DNA damage / vasculogenesis / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / positive regulation of cardiac muscle cell proliferation / cellular response to retinoic acid / keratinocyte differentiation / extrinsic apoptotic signaling pathway / positive regulation of epithelial cell proliferation / epithelial cell proliferation / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / positive regulation of canonical Wnt signaling pathway / cell-cell junction / regulation of cell population proliferation / positive regulation of cell growth / regulation of gene expression / protein-containing complex assembly / perikaryon / DNA-binding transcription factor binding / postsynaptic membrane / transcription regulator complex / cell population proliferation / 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 / negative regulation of gene expression / chromatin binding / dendrite / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dendrin / Nephrin and CD2AP-binding protein, Dendrin / : / Omega loop, TEAD interating 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: 2 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: Dendrin,Transcriptional coactivator YAP1
B: Dendrin,Transcriptional coactivator YAP1


Theoretical massNumber of molelcules
Total (without water)25,5362
Polymers25,5362
Non-polymers00
Water3,567198
1
A: Dendrin,Transcriptional coactivator YAP1


Theoretical massNumber of molelcules
Total (without water)12,7681
Polymers12,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dendrin,Transcriptional coactivator YAP1


Theoretical massNumber of molelcules
Total (without water)12,7681
Polymers12,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.376, 77.376, 116.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 12768.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Dendrin (residues 222-241 from Uniprot Q80TS7) linked YAP1 (residues 156-247 from Uniprot P46938)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ddn, Gm748, Kiaa0749, Yap1, Yap, Yap65 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80TS7, UniProt: P46938
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28-35% w/v pentaerythritol propoxylat 426 (5/4 PO/OH), 100mM HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 24702 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 32.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1210 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

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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: 6JK0

6jk0


Resolution: 2→29.191 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.21
RfactorNum. reflection% reflection
Rfree0.2111 1941 8.11 %
Rwork0.1853 --
obs0.1874 23948 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 0 198 1631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071487
X-RAY DIFFRACTIONf_angle_d1.1032043
X-RAY DIFFRACTIONf_dihedral_angle_d14.548537
X-RAY DIFFRACTIONf_chiral_restr0.043203
X-RAY DIFFRACTIONf_plane_restr0.005273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.05020.25241290.21711435X-RAY DIFFRACTION91
2.0502-2.10570.22621290.19351467X-RAY DIFFRACTION93
2.1057-2.16760.21791270.18841500X-RAY DIFFRACTION94
2.1676-2.23750.2241370.17911509X-RAY DIFFRACTION95
2.2375-2.31750.21931340.18421540X-RAY DIFFRACTION97
2.3175-2.41020.19561360.18571545X-RAY DIFFRACTION97
2.4102-2.51990.20651400.18661554X-RAY DIFFRACTION97
2.5199-2.65260.20821380.18841580X-RAY DIFFRACTION98
2.6526-2.81870.19931400.19741585X-RAY DIFFRACTION99
2.8187-3.03610.26051400.20561616X-RAY DIFFRACTION99
3.0361-3.34130.25371450.19931622X-RAY DIFFRACTION100
3.3413-3.82380.20791440.17381631X-RAY DIFFRACTION100
3.8238-4.81410.17821480.16031665X-RAY DIFFRACTION100
4.8141-29.19380.19211540.18871758X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 47.8898 Å / Origin y: 63.1532 Å / Origin z: 41.9106 Å
111213212223313233
T0.1619 Å20.0098 Å2-0.0395 Å2-0.1858 Å2-0.0048 Å2--0.1833 Å2
L1.5255 °2-0.7502 °20.3194 °2-0.9231 °20.2065 °2--1.7521 °2
S0.0118 Å °0.1826 Å °0.0339 Å °-0.1718 Å °-0.1726 Å °0.0405 Å °-0.2528 Å °0.0057 Å °0.1386 Å °
Refinement TLS groupSelection details: all

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