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- PDB-2d3j: NMR structure of the WIF domain from human WIF-1 -

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Basic information

Entry
Database: PDB / ID: 2d3j
TitleNMR structure of the WIF domain from human WIF-1
ComponentsWnt inhibitory factor-1
KeywordsSIGNALING PROTEIN INHIBITOR / palmitoyl group / recognition domain
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 / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Wnt inhibitory factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLiepinsh, E. / Banyai, L. / Patthy, L. / Otting, G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: NMR structure of the WIF domain of the human Wnt-inhibitory factor-1
Authors: Liepinsh, E. / Banyai, L. / Patthy, L. / Otting, G.
History
DepositionSep 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Wnt inhibitory factor-1


Theoretical massNumber of molelcules
Total (without water)17,5121
Polymers17,5121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Wnt inhibitory factor-1


Mass: 17511.961 Da / Num. of mol.: 1 / Fragment: WIF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5W5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D NOESY
1332D NOESY
143DQF-COSY
1532D TOCSY
162HNCA, CBCA(CO)NH
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM U-15N WIF DOMAIN90% H2O/10% D2O
20.7mM U-15N/13C WIF DOMAIN90% H2O/10% D2O
30.4mM U-15N WIF DOMAIN100% D2O
Sample conditionsIonic strength: no buffer added / pH: 6 / Pressure: ambient / Temperature: 301 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian UNITYVarianUNITY8002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
OPAL2.6Luginbuehlrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structure is based on 1755 NOE restraints and 413 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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