1Q4V

CRYSTAL STRUCTURE OF ALLO-ILEA2-INSULIN, AN INACTIVE CHIRAL ANALOGUE: IMPLICATIONS FOR THE MECHANISM OF RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of allo-Ile(A2)-insulin, an inactive chiral analogue: implications for the mechanism of receptor binding.

Wan, Z.L.Xu, B.Chu, Y.C.Katsoyannis, P.G.Weiss, M.A.

(2003) Biochemistry 42: 12770-12783

  • DOI: 10.1021/bi034430o
  • Primary Citation of Related Structures:  
    1Q4V

  • PubMed Abstract: 
  • The crystal structure of an inactive chiral analogue of insulin containing nonstandard substitution allo-Ile(A2) is described at 2.0 A resolution. In native insulin, the invariant Ile(A2) side chain anchors the N-terminal alpha-helix of the A-chain to th ...

    The crystal structure of an inactive chiral analogue of insulin containing nonstandard substitution allo-Ile(A2) is described at 2.0 A resolution. In native insulin, the invariant Ile(A2) side chain anchors the N-terminal alpha-helix of the A-chain to the hydrophobic core. The structure of the variant protein was determined by molecular replacement as a T(3)R(3) zinc hexamer. Whereas respective T- and R-state main-chain structures are similar to those of native insulin (main-chain root-mean-square deviations (RMSD) of 0.45 and 0.54 A, respectively), differences in core packing are observed near the variant side chain. The R-state core resembles that of the native R-state with a local inversion of A2 orientation (core side chain RMSD 0.75 A excluding A2); in the T-state, allo-Ile(A2) exhibits an altered conformation in association with the reorganization of the surrounding side chains (RMSD 0.98 A). Surprisingly, the core of the R-state is similar to that observed in solution nuclear magnetic resonance (NMR) studies of an engineered T-like monomer containing the same chiral substitution (allo-Ile(A2)-DKP-insulin; Xu, B., Hua, Q. X., Nakagawa, S. H., Jia, W., Chu, Y. C., Katsoyannis, P. G., and Weiss, M. A. (2002) J. Mol. Biol. 316, 435-441). Simulation of NOESY spectra based on crystallographic protomers enables the analysis of similarities and differences in solution. The different responses of the T- and R-state cores to chiral perturbation illustrates both their intrinsic plasticity and constraints imposed by hexamer assembly. Although variant T- and R-protomers retain nativelike protein surfaces, the receptor-binding activity of allo-Ile(A2)-insulin is low (2% relative to native insulin). This seeming paradox suggests that insulin undergoes a change in conformation to expose Ile(A2) at the hormone-receptor interface.


    Related Citations: 
    • CHIRAL MUTAGENESIS OF INSULIN'S HIDDEN RECEPTOR-BINDING SURFACE: STRUCTURE OF AN ALLO-ISOLEUCINE (A2) ANALOGUE
      Xu, B., Hua, Q.X., NAKAGAWA, S.H., JIA, W., CHU, Y.C., KASOYANNIS, P.G., WEISS, M.A.
      (2002) J Mol Biol 316: 435
    • A CAVITY-FORMING MUTATION IN INSULIN INDUCES SEGMENTAL UNFOLDING OF A SURROUNDING ALPHA-HELIX
      XU, B., HUA, Q.X., NAKAGAWA, S.H., JIA, W., CHU, Y.C., KATSOYANNIS, P.G., WEISS, M.A.
      (2002) Protein Sci 11: 104
    • NON-STANDARD INSULIN DESIGN: STRUCTURE-ACTIVITY RELATIONSHIPS AT THE PERIPHERY OF THE INSULIN Receptor
      WEISS, M.A., WAN, Z., ZHAO, M., CHU, Y.C., NAKAGAWA, S.H., BURKE, G.T., JIA, W., HELLMICH, R., KATSOYANNIS, P.G.
      (2002) J Mol Biol 315: 103
    • IS PROTEIN FOLDING HIERARCHIC? I. LOCAL STRUCTURE AND PEPTIDE FOLDING
      BALDWIN, R.L., ROSE, G.D.
      (1999) Trends Biochem Sci 24: 26
    • IS PROTEIN FOLDING HIERARCHIC? II. FOLDING INTERMEDIATES AND TRANSITION STATES
      BALDWIN, R.L., ROSE, G.D.
      (1999) Trends Biochem Sci 24: 77

    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin AC21N/AMutation(s): 1 
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
NIH Common Fund Data Resources
PHAROS:  P01308
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin BD30N/AMutation(s): 0 
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
NIH Common Fund Data Resources
PHAROS:  P01308
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPH
Query on IPH

Download Ideal Coordinates CCD File 
C
PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
IIL
Query on IIL
A,CL-PEPTIDE LINKINGC6 H13 N O2ILE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.487α = 90
b = 80.487β = 90
c = 37.939γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-19
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance