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- PDB-8a8q: Crystal structure of Protein Scalloped in complex with YAP peptide -

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Basic information

Entry
Database: PDB / ID: 8a8q
TitleCrystal structure of Protein Scalloped in complex with YAP peptide
Components
  • Isoform 7 of Transcriptional coactivator YAP1
  • Protein scalloped
KeywordsTRANSCRIPTION / Complex
Function / homology
Function and homology information


: / Transcriptional activation by YKI / : / imaginal disc-derived leg morphogenesis / somatic muscle development / compound eye morphogenesis / regulation of heart morphogenesis / wing disc development / enterocyte differentiation / regulation of keratinocyte proliferation ...: / Transcriptional activation by YKI / : / imaginal disc-derived leg morphogenesis / somatic muscle development / compound eye morphogenesis / regulation of heart morphogenesis / wing disc development / enterocyte differentiation / regulation of keratinocyte proliferation / imaginal disc-derived wing morphogenesis / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / 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 / sensory organ development / 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 / regulation of stem cell proliferation / hippo signaling / tissue homeostasis / 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 / cardiac muscle cell development / negative regulation of epithelial cell differentiation / negative regulation of neuroblast proliferation / 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 / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / canonical Wnt signaling pathway / vasculogenesis / embryonic organ development / positive regulation of osteoblast differentiation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / Nuclear signaling by ERBB4 / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / transcription corepressor binding / epithelial cell proliferation / stem cell proliferation / positive regulation of epithelial cell proliferation / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / transcription coactivator binding / positive regulation of protein localization to nucleus / RNA polymerase II transcription regulator complex / transcription corepressor activity / cell-cell junction / positive regulation of canonical Wnt signaling pathway / 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 / transcription regulator complex / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / 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 / nucleoplasm / membrane / nucleus / metal ion binding
Similarity search - Function
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 / WW domain ...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 / 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
ACETATE ION / Protein scalloped / Transcriptional coactivator YAP1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.465 Å
AuthorsScheufler, C. / Villard, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2023
Title: N-terminal beta-strand in YAP is critical for stronger binding to scalloped relative to TEAD transcription factor.
Authors: Fedir, B. / Yannick, M. / Marco, M. / Patrizia, F. / Catherine, Z. / Frederic, V. / Dirk, E. / Joerg, K. / Clemens, S. / Camilo, V.V. / Patrick, C.
History
DepositionJun 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein scalloped
B: Protein scalloped
C: Isoform 7 of Transcriptional coactivator YAP1
D: Isoform 7 of Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6266
Polymers62,5084
Non-polymers1182
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-44 kcal/mol
Surface area22990 Å2
Unit cell
Length a, b, c (Å)42.772, 85.7, 76.227
Angle α, β, γ (deg.)90, 92.62, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein scalloped


Mass: 25757.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sd, CG8544
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P30052
#2: Protein Isoform 7 of Transcriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 5496.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P46937
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6 20 % PEG8000 0.2 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.472→76.147 Å / Num. obs: 52439 / % possible obs: 56.5 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.041 / Rrim(I) all: 0.094 / Net I/σ(I): 10.1
Reflection shellResolution: 1.472→1.673 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2623 / CC1/2: 0.63 / Rpim(I) all: 0.397 / Rrim(I) all: 0.8 / % possible all: 8.9

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (3-FEB-2022)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Previous in-house structure.

Resolution: 1.465→29.09 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.118
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 2624 -RANDOM
Rwork0.2108 ---
obs0.2119 52431 55.7 %-
Displacement parametersBiso mean: 21.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.2285 Å20 Å21.7681 Å2
2--1.8161 Å20 Å2
3----1.5876 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.465→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 8 235 4199
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084057HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.995482HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1391SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes683HARMONIC5
X-RAY DIFFRACTIONt_it4057HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion529SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3312SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.92
X-RAY DIFFRACTIONt_other_torsion14.94
LS refinement shellResolution: 1.47→1.6 Å
RfactorNum. reflection% reflection
Rfree0.2888 57 -
Rwork0.2775 --
obs0.2781 1049 4.74 %
Refinement TLS params.

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)
10.17850.1289-0.15460.29220.10951.22210.03030.0135-0.02370.0135-0.0006-0.0636-0.0237-0.0636-0.0297-0.0488-0.01180.01640.03710.0004-0.0331-4.7459-12.3442-28.9873
20.40840.1194-0.35190.3488-0.0271.9368-0.0368-0.06640.2254-0.0664-0.01070.10420.22540.10420.04750.00780.03410.024-0.00940.0179-0.06488.8368-23.87951.4305
30.41270.0871-0.33970.7471-0.26752.5801-0.0214-0.0406-0.0145-0.0406-0.04010.192-0.01450.1920.0615-0.0750.01140.0158-0.0024-0.0041-0.07454.2752-16.671-38.5153
40.53010.24830.09570.6152-0.24472.16280.01680.0619-0.09550.0619-0.08490.0208-0.09550.02080.0682-0.03930.02650.03040.0073-0.0045-0.08211.9136-17.074811.368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A223 - 440
2X-RAY DIFFRACTION1{ A|* }A501
3X-RAY DIFFRACTION2{ B|* }B224 - 440
4X-RAY DIFFRACTION2{ B|* }B501
5X-RAY DIFFRACTION3{ C|* }C51 - 99
6X-RAY DIFFRACTION4{ D|* }D51 - 99

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