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- PDB-6xtz: Structure of Dally-like protein in complex with O-palmitoleoyl serine -

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Basic information

Entry
Database: PDB / ID: 6xtz
TitleStructure of Dally-like protein in complex with O-palmitoleoyl serine
ComponentsDally-like, isoform A
KeywordsSIGNALING PROTEIN / Glypicans / GPI-anchored / Wnt / palmitoleate
Function / homology
Function and homology information


perivitelline space / Signaling by ROBO receptors / regulation of presynapse organization / HS-GAG biosynthesis / HS-GAG degradation / cytoneme / regulation of imaginal disc growth / imaginal disc-derived wing margin morphogenesis / A tetrasaccharide linker sequence is required for GAG synthesis / wing disc dorsal/ventral pattern formation ...perivitelline space / Signaling by ROBO receptors / regulation of presynapse organization / HS-GAG biosynthesis / HS-GAG degradation / cytoneme / regulation of imaginal disc growth / imaginal disc-derived wing margin morphogenesis / A tetrasaccharide linker sequence is required for GAG synthesis / wing disc dorsal/ventral pattern formation / regulation of protein localization to membrane / epithelial cell migration, open tracheal system / compound eye development / segment polarity determination / hedgehog family protein binding / segment specification / positive regulation of fibroblast growth factor receptor signaling pathway / Wnt-protein binding / positive regulation of smoothened signaling pathway / neuromuscular junction development / positive regulation of Wnt signaling pathway / axon guidance / neuromuscular junction / cell migration / positive regulation of canonical Wnt signaling pathway / collagen-containing extracellular matrix / external side of plasma membrane / axon / synapse / cell surface / plasma membrane
Similarity search - Function
O-palmitoleoyl serine / Dally-like, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsVecchia, L. / Jones, E.Y.
Funding support United Kingdom, European Union, 7items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001204 United Kingdom
European Union (EU)294523European Union
European Union (EU)647278European Union
Cancer Research UKC375/A17721 United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
Wellcome Trust102164/B/13/Z United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
CitationJournal: Nature / Year: 2020
Title: Glypicans shield the Wnt lipid moiety to enable signalling at a distance.
Authors: McGough, I.J. / Vecchia, L. / Bishop, B. / Malinauskas, T. / Beckett, K. / Joshi, D. / O'Reilly, N. / Siebold, C. / Jones, E.Y. / Vincent, J.P.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Aug 26, 2020Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: entity / entity_poly ...entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code ..._entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.host_org_common_name / _pdbx_poly_seq_scheme.mon_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id
Revision 2.1Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 3.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_asym
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id
Revision 3.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dally-like, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7958
Polymers62,7421
Non-polymers1,0537
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint2 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.691, 77.380, 118.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Dally-like, isoform A / LD47466p


Mass: 62742.180 Da / Num. of mol.: 1 / Mutation: K398Q, K399A, R402Q, R438Q, R441A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: dlp, CG17703, CG5031, CT16138, D-gpcB, Dally-like, DLP, Dlp, Dly, dly, Dmel\CG32146, CG32146, Dmel_CG32146
Production host: Homo sapiens (human) / References: UniProt: Q9VUG1
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 88 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-O18 / O-palmitoleoyl serine / (2S)-2-azanyl-3-[(Z)-hexadec-9-enoyl]oxy-propanoic acid


Mass: 341.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H35NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 16.25% (w/v) PEG4000, 0.1 M MMT pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97954 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.21→56.14 Å / Num. obs: 30164 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 42.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 8
Reflection shellResolution: 2.21→2.25 Å / Num. unique obs: 1459 / CC1/2: 0.685

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Processing

Software
NameVersionClassification
PHENIXdev_3488refinement
PHENIXdev_3488refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ODN

3odn


Resolution: 2.21→56.14 Å / SU ML: 0.3133 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6936
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2551 1531 5.1 %
Rwork0.2266 28496 -
obs0.2281 30027 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.93 Å2
Refinement stepCycle: LAST / Resolution: 2.21→56.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 69 82 3514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163528
X-RAY DIFFRACTIONf_angle_d0.36954746
X-RAY DIFFRACTIONf_chiral_restr0.0324514
X-RAY DIFFRACTIONf_plane_restr0.0022614
X-RAY DIFFRACTIONf_dihedral_angle_d13.25972159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.280.37941550.36462532X-RAY DIFFRACTION99.7
2.28-2.360.37851420.32822524X-RAY DIFFRACTION99.44
2.36-2.460.36211550.30482528X-RAY DIFFRACTION99.48
2.46-2.570.2911170.272572X-RAY DIFFRACTION99.63
2.57-2.70.26821320.262562X-RAY DIFFRACTION99.67
2.7-2.870.32461530.24632558X-RAY DIFFRACTION99.71
2.87-3.10.31711390.24732568X-RAY DIFFRACTION99.89
3.1-3.410.26851310.24342598X-RAY DIFFRACTION99.96
3.41-3.90.25541260.21682645X-RAY DIFFRACTION99.96
3.9-4.910.21281310.17812655X-RAY DIFFRACTION99.96
4.91-56.140.18281500.19912754X-RAY DIFFRACTION99.55
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)
10.275545692606-0.122543571402-0.0189702161030.6636438815710.195554677150.5399204097230.002932102164330.0821793898416-0.0982271815065-0.02673446946660.0935769214885-0.2545923612190.1482184280140.061372764912-2.44324780108E-50.3668777736070.0102102450794-0.001973371279670.405810403978-0.03170227876460.4025225904511.4759602689-21.3671676732-9.66987240327
20.094343808396-0.0368472076403-0.08369953281830.02007127090430.06271428704130.2003528471310.0833202196114-0.3669986867460.1856042798880.348649743167-0.425577744249-0.0941069136599-0.175754863027-0.3362930387290.0003160902378790.550089715690.00362769788917-0.004839640345990.502073221101-0.0778962048080.7082777245649.4270797652720.086491091610.0909894172
30.1777343526860.203155645439-0.1625851090730.263853435433-0.1916100656480.516998031943-0.12811759699-0.6335302342580.6799145426880.1570184860910.124155362462-0.208844609463-0.45457280903-0.2584696424170.1315092487020.8704168379060.164224550329-0.01700170445120.73286228091-0.3282011973810.7318767393987.2137902497830.347037272416.283237307
40.1368669573140.1499032612120.01942817931850.4750240571040.5530505656170.947732846262-0.0271488323817-0.009419668210320.0336317097781-0.375548786747-0.04043436195240.0302603008963-0.0567167273334-0.06878395921982.48425079112E-50.2972037982570.00606830454494-0.03604221573280.367423724582-0.01377966381190.4332091152033.35178985655-9.9159653217-9.44160973288
50.9521088127040.2754142221550.1162757705651.18188134444-0.3127477113970.524969590903-0.2133924315590.09045477740080.238583015306-0.5467310363260.2691489827860.217092077333-0.3184410842590.07349255333120.1099043212990.4286302099560.04776558095060.02854862119720.3817061411990.03470503233240.455494481796.926840273642.56884768369-8.51415998571
60.09027190333140.05374082173770.02275897704860.4969367566720.03626070332190.2871084790690.256828326397-0.0121009039687-0.263814753907-0.316627582455-0.3237948888050.388092725132-0.0131489592238-0.4658656985780.0008417339865110.6078311878560.00616656419615-0.03781083755850.449239203815-0.06804291931720.538522707753-6.81901450601-34.9079091699-21.2454595233
70.1830519166760.0471893951787-0.1004711237540.06016008536560.09176420768490.302628242379-0.118019487467-0.1067876958150.146915370113-0.0748287632840.1585764369220.07108640459140.0678489673841-0.128925954984.2875188146E-50.3360363092210.00117056337009-0.0126416959390.462115220219-0.04746339645780.422972377165-1.51522030102-11.8376204135-0.668610449608
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 75 through 204 )
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 228 )
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 254 )
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 379 )
5X-RAY DIFFRACTION5chain 'A' and (resid 380 through 539 )
6X-RAY DIFFRACTION6chain 'A' and (resid 540 through 582 )
7X-RAY DIFFRACTION7chain 'A' and (resid 583 through 611 )

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