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 2JM2 | pdb_00002jm2

Structure of the N-terminal subdomain of insulin-like growth factor (IGF) binding protein-6 and its interactions with IGFs


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.7 of the entry. See complete history. 

Literature

The N-Terminal Subdomain of Insulin-like Growth Factor (IGF) Binding Protein 6. Structure and Interaction with IGFs

Chandrashekaran, I.R., Yao, S., Wang, C.C., Bansal, P.S., Alewood, P.F., Forbes, B.E., Wallace, J.C., Bach, L.A., Norton, R.S.

(2007) Biochemistry 46: 3065-3074

  • DOI: https://doi.org/10.1021/bi0619876
  • Primary Citation Related Structures: 
    2JM2

  • PubMed Abstract: 

    Insulin-like growth factor binding proteins (IGFBPs) modulate the activity and distribution of insulin-like growth factors (IGFs). IGFBP-6 differs from other IGFBPs in being a relatively specific inhibitor of IGF-II actions. Another distinctive feature of IGFBP-6 is its unique N-terminal disulfide linkages; the N-domains of IGFBPs 1-5 contain six disulfides and share a conserved GCGCC motif, but IGFBP-6 lacks the two adjacent cysteines in this motif, so its first three N-terminal disulfide linkages differ from those of the other IGFBPs. The contributions of the N- and C-domains of IGFBP-6 to its IGF binding properties and their structure-function relationships have been characterized in part, but the structure and function of the distinctive N-terminal subdomain of IGFBP-6 are unknown. Here we report the solution structure of a polypeptide corresponding to residues 1-45 of the N-terminal subdomain of IGFBP-6 (NN-BP-6). The extended structure of the N-terminal subdomain of IGFBP-6 is very different from that of the short two-stranded beta-sheet of the N-terminal subdomain of IGFBP-4 and, by implication, the other IGFBPs. NN-BP-6 contains a potential cation-binding motif; lanthanide ion binding was observed, but no significant interaction was found with physiologically relevant metal ions like calcium or magnesium. However, this subdomain of IGFBP-6 has a higher affinity for IGF-II than IGF-I, suggesting that it may contribute to the marked IGF-II binding preference of IGFBP-6. The extended structure and flexibility of this subdomain of IGFBP-6 could play a role in enhancing the rate of ligand association and thereby be significant in IGF recognition.


  • Organizational Affiliation: 
    • The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3050, Australia.

Macromolecule Content 

  • Total Structure Weight: 4.37 kDa 
  • Atom Count: 299 
  • Modeled Residue Count: 45 
  • Deposited Residue Count: 45 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Insulin-like growth factor-binding protein 645Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P24592 (Homo sapiens)
Explore P24592 
Go to UniProtKB:  P24592
PHAROS:  P24592
GTEx:  ENSG00000167779 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24592
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-02-05
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other, Source and taxonomy
  • Version 1.4: 2022-10-05
    Changes: Data collection, Database references, Experimental preparation, Refinement description, Source and taxonomy, Structure summary
  • Version 1.5: 2023-06-14
    Changes: Other
  • Version 1.6: 2023-12-20
    Changes: Data collection, Other
  • Version 1.7: 2024-11-20
    Changes: Database references, Structure summary