2D3J | pdb_00002d3j

NMR structure of the WIF domain from human WIF-1

• PDB DOI: https://doi.org/10.2210/pdb2D3J/pdb

• Classification: SIGNALING PROTEIN INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-29 Released: 2006-04-25 
• Deposition Author(s): Liepinsh, E., Banyai, L., Patthy, L., Otting, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

NMR structure of the WIF domain of the human Wnt-inhibitory factor-1

Liepinsh, E., Banyai, L., Patthy, L., Otting, G.

(2006) J Mol Biology 357: 942-950

• PubMed: 16476441 
• DOI: https://doi.org/10.1016/j.jmb.2006.01.047
• Primary Citation Related Structures: 
  2D3J


• PubMed Abstract: 
  

  The human Wnt-binding protein Wnt-inhibitory factor-1 (WIF-1) comprises an N-terminal WIF module followed by five EGF-like repeats. Here we report the three-dimensional structure of the WIF domain of WIF-1 determined by NMR spectroscopy. The fold consists of an eight-stranded beta-sandwich reminiscent of the immunoglobulin fold. Residual detergent (Brij-35) used in the refolding protocol was found to bind tightly to the WIF domain. The binding site was identified by intermolecular nuclear Overhauser effects observed between the WIF domain and the alkyl chain of the detergent. The results point to a possible role of WIF domains as a recognition motif of Wnt and Drosophila Hedgehog proteins that are activated by palmitoylation.

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Organizational Affiliation: 
• Institute of Organic Synthesis, LV-1006 Riga, Latvia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.51 kDa 
• Atom Count: 1,231 
• Modeled Residue Count: 157 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Wnt inhibitory factor-1	A	157	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5W5 (Homo sapiens) Explore Q9Y5W5  Go to UniProtKB:  Q9Y5W5
PHAROS:  Q9Y5W5 GTEx:  ENSG00000156076

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-25 
Deposition Author(s): Liepinsh, E., Banyai, L., Patthy, L., Otting, G.

Revision History  

• Version 1.0: 2006-04-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary