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- PDB-4rex: Crystal structure of the first WW domain of human YAP2 isoform -

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Basic information

Entry
Database: PDB / ID: 4rex
TitleCrystal structure of the first WW domain of human YAP2 isoform
ComponentsYorkie homolog
KeywordsPROTEIN BINDING / WW domain / Hippo signaling pathway / antiparallel beta-sheet / proline rich motifs
Function / homology
Function and homology information


enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / tissue homeostasis / hippo signaling / regulation of stem cell proliferation / EGR2 and SOX10-mediated initiation of Schwann cell myelination / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / Signaling by Hippo / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial cell differentiation / negative regulation of fat cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / Nuclear signaling by ERBB4 / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / response to progesterone / epithelial cell proliferation / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / cellular response to gamma radiation / wound healing / cell morphogenesis / positive regulation of protein localization to nucleus / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / cell-cell junction / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription factor binding / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / DNA damage response / chromatin binding / 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 / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Transcriptional coactivator YAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsCamara-Artigas, A.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal structure of the first WW domain of human YAP2 isoform.
Authors: Martinez-Rodriguez, S. / Bacarizo, J. / Luque, I. / Camara-Artigas, A.
History
DepositionSep 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Sep 20, 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 / software / 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 / _software.name / _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

Downloads & links

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Assembly

Deposited unit
A: Yorkie homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6252
Polymers5,5291
Non-polymers961
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.673, 43.101, 21.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-420-

HOH

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Components

#1: Protein/peptide Yorkie homolog / 65 kDa Yes-associated protein / YAP65


Mass: 5529.180 Da / Num. of mol.: 1 / Fragment: WW domain (UNP residues 165-209)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YAP1, YAP65 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46937
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.77 Å3/Da / Density % sol: 30.57 %
Crystal growTemperature: 293 K / pH: 5
Details: 1.5 M ammonium sulphate, 0.1 M sodium acetate, 100 mM proline, 5 mM NDSB-201 and 5mM MBCD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2013
Details: SI(111) CHANNEL-CUT CRYSTAL MONOCHROMATOR AND A PAIR OF KB MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Number: 38300 / Rmerge(I) obs: 0.104 / D res high: 1.6 Å / D res low: 42.67 Å / Num. obs: 5514 / % possible obs: 99.2 / Rejects: 10
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
1.61.6310.5826.8
8.3142.6710.0574.9
ReflectionResolution: 1.6→42.67 Å / Num. obs: 5514 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 12.78 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 12
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 3.2 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.13data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HO2

2ho2


Resolution: 1.6→21.551 Å / SU ML: 0.16 / σ(F): 0.47 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1942 452 4.57 %
Rwork0.1776 --
obs0.1785 9891 98.83 %
all-10001 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.7 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms378 0 5 42 425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011401
X-RAY DIFFRACTIONf_angle_d1.356547
X-RAY DIFFRACTIONf_dihedral_angle_d14.606145
X-RAY DIFFRACTIONf_chiral_restr0.05656
X-RAY DIFFRACTIONf_plane_restr0.00971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6004-1.83190.24081480.19993151X-RAY DIFFRACTION99
1.8319-2.30760.18981390.19113114X-RAY DIFFRACTION98
2.3076-21.55240.18461650.16513174X-RAY DIFFRACTION99
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)
10.2256-0.06260.07820.0384-0.05340.08290.0401-0.00470.14430.09290.01850.0463-0.0430.0772-0.01210.1527-0.01640.00380.1284-0.01530.107714.750951.955150.5746
20.05210.04060.03930.09850.05170.03470.13760.0665-0.0393-0.0387-0.0089-0.0714-0.05710.0320.03020.10260.0110.01220.1192-0.01120.102512.93439.648549.5999
30.07580.07920.00040.46250.14160.0905-0.03720.0258-0.0209-0.08230.05230.11670.0408-0.0419-0.00640.075-0.00690.00020.08830.00170.08845.552139.977752.2023
40.0851-0.07090.17570.0996-0.0990.41140.12520.12320.1760.02960.11330.1164-0.02360.1420.0510.1525-0.0304-0.00120.1156-0.01340.19745.793553.99152.7601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 175 )
2X-RAY DIFFRACTION2chain 'A' and (resid 176 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 201 )
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 208 )

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