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- PDB-2ygq: WIF domain-epidermal growth factor (EGF)-like domains 1-3 of huma... -

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Basic information

Entry
Database: PDB / ID: 2ygq
TitleWIF domain-epidermal growth factor (EGF)-like domains 1-3 of human Wnt inhibitory factor 1 in complex with 1,2- dipalmitoylphosphatidylcholine
ComponentsWNT INHIBITORY FACTOR 1
KeywordsSIGNALING PROTEIN / WNT SIGNALING PATHWAY / WNT ANTAGONIST / MORPHOGEN / CANCER / GLYCOSAMINOGLYCAN
Function / homology
Function and homology information


Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Wnt-protein binding / negative regulation of Wnt signaling pathway / positive regulation of fat cell differentiation / TCF dependent signaling in response to WNT / Wnt signaling pathway / signaling receptor binding / cell surface / signal transduction / extracellular region
Similarity search - Function
Wnt inhibitory factor (WIF)-1 / : / Wnt, WIF domain / WIF domain / WIF domain superfamily / WIF domain / WIF domain profile. / Wnt-inhibitory factor-1 like domain / Delta-like/Jagged, EGF-like domain / EGF-like, conserved site ...Wnt inhibitory factor (WIF)-1 / : / Wnt, WIF domain / WIF domain / WIF domain superfamily / WIF domain / WIF domain profile. / Wnt-inhibitory factor-1 like domain / Delta-like/Jagged, EGF-like domain / EGF-like, conserved site / Human growth factor-like EGF / Laminin / Laminin / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
sucrose octasulfate / alpha-L-fucopyranose / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Wnt inhibitory factor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.951 Å
AuthorsMalinauskas, T. / Aricescu, A.R. / Lu, W. / Siebold, C. / Jones, E.Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Modular Mechanism of Wnt Signaling Inhibition by Wnt Inhibitory Factor 1
Authors: Malinauskas, T. / Aricescu, A.R. / Lu, W. / Siebold, C. / Jones, E.Y.
History
DepositionApr 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / 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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WNT INHIBITORY FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7256
Polymers35,4021
Non-polymers2,3235
Water00
1
A: WNT INHIBITORY FACTOR 1
hetero molecules

A: WNT INHIBITORY FACTOR 1
hetero molecules

A: WNT INHIBITORY FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,17518
Polymers106,2053
Non-polymers6,97015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area14990 Å2
ΔGint-81.4 kcal/mol
Surface area37340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.007, 178.007, 178.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein WNT INHIBITORY FACTOR 1 / WIF-1


Mass: 35401.625 Da / Num. of mol.: 1 / Fragment: WIF DOMAIN-EGF-LIKE DOMAINS 1-5, RESIDUES 35-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Cell line (production host): N-ACETYLGLUCOSAMINYLTRANSFERASE I-NEGATIVE HEK 293S GNTI(-)CELLS
Production host: HOMO SAPIENS (human) / References: UniProt: Q9Y5W5
#2: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P
#4: 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.: 2
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
#5: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY
Sequence detailsISOFORM Q166K. THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND C-TERMINAL NINE AMINO ACID ...ISOFORM Q166K. THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND C-TERMINAL NINE AMINO ACID RESIDUES (GTKHHHHHH) OF THE CRYSTALLISATION CONSTRUCT ARE DERIVED FROM THE PHLSEC VECTOR.

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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: 8.53 Å3/Da / Density % sol: 82 % / Description: NONE
Crystal growpH: 5.7
Details: 0.75 M SODIUM SUCCINATE PH 5.7, 35 MG/ML SUCROSE OCTASULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.95→40 Å / Num. obs: 8403 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 27.2
Reflection shellResolution: 3.95→4.09 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.951→39.804 Å / SU ML: 0.63 / σ(F): 0 / Phase error: 29.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3306 382 4.8 %
Rwork0.297 --
obs0.2985 8048 95.96 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 184.367 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.951→39.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 143 0 1969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142027
X-RAY DIFFRACTIONf_angle_d2.0872742
X-RAY DIFFRACTIONf_dihedral_angle_d28.521833
X-RAY DIFFRACTIONf_chiral_restr0.122291
X-RAY DIFFRACTIONf_plane_restr0.011343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9508-4.52180.32021100.31652415X-RAY DIFFRACTION91
4.5218-5.69440.2811310.28342566X-RAY DIFFRACTION97
5.6944-39.80560.35781410.29752685X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 30.9997 Å / Origin y: 4.4045 Å / Origin z: 14.9562 Å
111213212223313233
T1.1011 Å20.0253 Å20.2386 Å2-1.0649 Å20.0784 Å2--1.1069 Å2
L1.72 °2-0.767 °2-0.6516 °2-1.9007 °2-1.1107 °2--1.8936 °2
S-0.046 Å °-0.3552 Å °-0.261 Å °0.6898 Å °0.1429 Å °0.1029 Å °-0.2222 Å °0.3645 Å °-0.0867 Å °
Refinement TLS groupSelection details: ALL

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