Movatterモバイル変換


[0]ホーム

URL:


RCSB PDB
249,324
Structures from the PDB archive
1,068,577
Computed Structure Models (CSM)
  • PDB-101
  • wwPDB
  • EMDataResource
  • NAKB: Nucleic Acid Knowledgebase
  • wwPDB Foundation
  • PDB-IHM Logo

 2DSP|pdb_00002dsp

Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for the inhibition of insulin-like growth factors by insulin-like growth factor-binding proteins.

Sitar, T.Popowicz, G.M.Siwanowicz, I.Huber, R.Holak, T.A.

(2006) Proc Natl Acad Sci U S A 103: 13028-13033

  • PubMed16924115 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1073/pnas.0605652103
  • Primary Citation of Related Structures:  
    2DSP,2DSQ,2DSR

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany.
Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 


Find Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA (software)

PreviousNext

Macromolecule Content 

  • Total Structure Weight: 17.49 kDa 
  • Atom Count: 1,100 
  • Modeled Residue Count: 148 
  • Deposited Residue Count: 162 
  • Unique protein chains: 2

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin-like growth factor-binding protein 4A [auth B]92Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22692
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin-like growth factor IBB [auth I]70Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05019
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work: 0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.33α = 90
b = 38.99β = 99.89
c = 61.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-22
    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: 2023-10-25
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary
  • RCSB PDB is hosted by

  • The Rutgers Artificial Intelligence and Data Science Collaboratory logo
    Uiversity of California San Diego logoSan Diego Supercomputer Center logo
    University of California San Francisco Logo

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.


[8]ページ先頭

©2009-2026 Movatter.jp