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- PDB-6y20: Crystal structure of Protein Scalloped (222-440) bound to Protein... -

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Basic information

Entry
Database: PDB / ID: 6y20
TitleCrystal structure of Protein Scalloped (222-440) bound to Protein Vestigial (298-337)
Components
  • (Protein scalloped) x 2
  • Protein vestigial
KeywordsTRANSCRIPTION / Complex
Function / homology
Function and homology information


dorsal/ventral lineage restriction, imaginal disc / determination of muscle attachment site / cell elongation involved in imaginal disc-derived wing morphogenesis / : / Transcriptional activation by YKI / : / wing disc proximal/distal pattern formation / haltere development / wing disc dorsal/ventral pattern formation / imaginal disc-derived leg morphogenesis ...dorsal/ventral lineage restriction, imaginal disc / determination of muscle attachment site / cell elongation involved in imaginal disc-derived wing morphogenesis / : / Transcriptional activation by YKI / : / wing disc proximal/distal pattern formation / haltere development / wing disc dorsal/ventral pattern formation / imaginal disc-derived leg morphogenesis / somatic muscle development / compound eye morphogenesis / regulation of heart morphogenesis / wing disc morphogenesis / wing disc development / imaginal disc-derived wing morphogenesis / : / sensory organ development / hippo signaling / cardiac muscle cell development / negative regulation of neuroblast proliferation / embryonic organ development / regulation of mitotic cell cycle / transcription corepressor binding / stem cell proliferation / transcription coactivator binding / RNA polymerase II transcription regulator complex / regulation of cell population proliferation / DNA replication / transcription regulator complex / 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 DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Vestigial family / Vestigial/Tondu family / TDU repeat / Short repeats in human TONDU, fly vestigial and other proteins. / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. ...Vestigial family / Vestigial/Tondu family / TDU repeat / Short repeats in human TONDU, fly vestigial and other proteins. / 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
Similarity search - Domain/homology
MYRISTIC ACID / Protein scalloped / Protein vestigial
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsScheufler, C. / Villard, F. / Bokhovchuk, F.
CitationJournal: Sci Rep / Year: 2020
Title: A new perspective on the interaction between the Vg/VGLL1-3 proteins and the TEAD transcription factors.
Authors: Mesrouze, Y. / Aguilar, G. / Bokhovchuk, F. / Martin, T. / Delaunay, C. / Villard, F. / Meyerhofer, M. / Zimmermann, C. / Fontana, P. / Wille, R. / Vorherr, T. / Erdmann, D. / Furet, P. / ...Authors: Mesrouze, Y. / Aguilar, G. / Bokhovchuk, F. / Martin, T. / Delaunay, C. / Villard, F. / Meyerhofer, M. / Zimmermann, C. / Fontana, P. / Wille, R. / Vorherr, T. / Erdmann, D. / Furet, P. / Scheufler, C. / Schmelzle, T. / Affolter, M. / Chene, P.
History
DepositionFeb 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: 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
Revision 2.0May 29, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein scalloped
B: Protein scalloped
C: Protein vestigial
D: Protein vestigial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7765
Polymers60,5474
Non-polymers2281
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-28 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.23, 62.039, 156.887
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein scalloped


Mass: 25757.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sd, CG8544 / Production host: Escherichia coli (E. coli) / References: UniProt: P30052
#2: Protein Protein scalloped


Mass: 25548.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sd, CG8544 / Production host: Escherichia coli (E. coli) / References: UniProt: P30052
#3: Protein/peptide Protein vestigial


Mass: 4620.899 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q26366
#4: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 1.94 Å3/Da / Density % sol: 36.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Magnesium chloride, 0.1 M Bis-Tris pH 6.5, 25% PEG3350

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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 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.851→78.444 Å / Num. obs: 30608 / % possible obs: 74.6 % / Redundancy: 16.7 % / CC1/2: 0.994 / Net I/σ(I): 9.337
Reflection shellResolution: 1.851→2.013 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1531 / CC1/2: 0.619 / % possible all: 16.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (3-OCT-2019)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6q36

6q36


Resolution: 1.849→78 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.215 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.171 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 1464 -RANDOM
Rwork0.1877 ---
obs0.1894 30586 74.3 %-
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.9551 Å20 Å20 Å2
2---0.0739 Å20 Å2
3----0.8811 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.849→78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 18 255 4223
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084106HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.995550HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1436SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes705HARMONIC5
X-RAY DIFFRACTIONt_it4106HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion529SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3538SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion16.25
LS refinement shellResolution: 1.85→2 Å
RfactorNum. reflection% reflection
Rfree0.2908 28 -
Rwork0.2383 --
obs0.2406 612 9.71 %
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)
11.62790.17450.21960.7193-0.06410.8508-0.0506-0.0272-0.041-0.02720.0333-0.0289-0.041-0.02890.0173-0.041-0.004-0.001-0.08380.0006-0.0271-4.81116.9146-29.2213
21.3307-0.2155-0.44521.22960.42441.5883-0.02220.13590.1760.13590.0666-0.03010.176-0.0301-0.0445-0.0077-0.0114-0.0055-0.07160.0041-0.056-9.6267-6.8955-12.1118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* C|* }
2X-RAY DIFFRACTION2{ B|* D|* }

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