Experimental Data Snapshot
Starting Model:experimental
View more details
wwPDB Validation  3D Report Full Report
(2006) Proc Natl Acad Sci U S A 103: 13028-13033
Insulin-like growth factor-binding proteins (IGFBPs) control bioavailability, activity, and distribution of insulin-like growth factor (IGF)1 and -2 through high-affinity IGFBP/IGF complexes. IGF-binding sites are found on N- and C-terminal fragments of IGFBPs, the two conserved domains of IGFBPs. The relative contributions of these domains to IGFBP/IGF complexation has been difficult to analyze, in part, because of the lack of appropriate three-dimensional structures. To analyze the effects of N- and C-terminal domain interactions, we determined several x-ray structures: first, of a ternary complex of N- and C-terminal domain fragments of IGFBP4 and IGF1 and second, of a "hybrid" ternary complex using the C-terminal domain fragment of IGFBP1 instead of IGFBP4. We also solved the binary complex of the N-terminal domains of IGFBP4 and IGF1, again to analyze C- and N-terminal domain interactions by comparison with the ternary complexes. The structures reveal the mechanisms of IGF signaling regulation via IGFBP binding. This finding supports research into the design of IGFBP variants as therapeutic IGF inhibitors for diseases of IGF disregulation. In IGFBP4, residues 1-38 form a rigid disulphide bond ladder-like structure, and the first five N-terminal residues bind to IGF and partially mask IGF residues responsible for the type 1 IGF receptor binding. A high-affinity IGF1-binding site is located in a globular structure between residues 39 and 82. Although the C-terminal domains do not form stable binary complexes with either IGF1 or the N-terminal domain of IGFBP4, in the ternary complex, the C-terminal domain contacts both and contributes to blocking of the IGF1 receptor-binding region of IGF1.
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Insulin-like growth factor-binding protein 4 | A [auth B] | 92 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P22692 (Homo sapiens) Explore P22692  Go to UniProtKB:  P22692 | |||||
PHAROS:  P22692 GTEx:  ENSG00000141753  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P22692 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Insulin-like growth factor IB | B [auth I] | 70 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P05019 (Homo sapiens) Explore P05019  Go to UniProtKB:  P05019 | |||||
PHAROS:  P05019 GTEx:  ENSG00000017427  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P05019 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 32.33 | α = 90 |
| b = 38.99 | β = 99.89 |
| c = 61.33 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.