3GKY | pdb_00003gky

The Structural Basis of an ER Stress-Associated Bottleneck in a Protein Folding Landscape


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.253 (Depositor) 
  • R-Value Work: 
    0.209 (Depositor), 0.234 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3GKY

This is version 1.4 of the entry. See complete history

Literature

Crystal structure of a "nonfoldable" insulin: IMPAIRED FOLDING EFFICIENCY DESPITE NATIVE ACTIVITY.

Liu, M.Wan, Z.L.Chu, Y.C.Aladdin, H.Klaproth, B.Choquette, M.Hua, Q.X.Mackin, R.B.Rao, J.S.De Meyts, P.Katsoyannis, P.G.Arvan, P.Weiss, M.A.

(2009) J Biological Chem 284: 35259-35272

  • DOI: https://doi.org/10.1074/jbc.M109.046888
  • Primary Citation Related Structures: 
    3GKY

  • PubMed Abstract: 

    Protein evolution is constrained by folding efficiency ("foldability") and the implicit threat of toxic misfolding. A model is provided by proinsulin, whose misfolding is associated with beta-cell dysfunction and diabetes mellitus. An insulin analogue containing a subtle core substitution (Leu(A16) --> Val) is biologically active, and its crystal structure recapitulates that of the wild-type protein. As a seeming paradox, however, Val(A16) blocks both insulin chain combination and the in vitro refolding of proinsulin. Disulfide pairing in mammalian cell culture is likewise inefficient, leading to misfolding, endoplasmic reticular stress, and proteosome-mediated degradation. Val(A16) destabilizes the native state and so presumably perturbs a partial fold that directs initial disulfide pairing. Substitutions elsewhere in the core similarly destabilize the native state but, unlike Val(A16), preserve folding efficiency. We propose that Leu(A16) stabilizes nonlocal interactions between nascent alpha-helices in the A- and B-domains to facilitate initial pairing of Cys(A20) and Cys(B19), thus surmounting their wide separation in sequence. Although Val(A16) is likely to destabilize this proto-core, its structural effects are mitigated once folding is achieved. Classical studies of insulin chain combination in vitro have illuminated the impact of off-pathway reactions on the efficiency of native disulfide pairing. The capability of a polypeptide sequence to fold within the endoplasmic reticulum may likewise be influenced by kinetic or thermodynamic partitioning among on- and off-pathway disulfide intermediates. The properties of [Val(A16)]insulin and [Val(A16)]proinsulin demonstrate that essential contributions of conserved residues to folding may be inapparent once the native state is achieved.


  • Organizational Affiliation
    • Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA.

Macromolecule Content 

  • Total Structure Weight: 11.92 kDa 
  • Atom Count: 958 
  • Modeled Residue Count: 102 
  • Deposited Residue Count: 102 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Insulin A chain
A, C
21Sus scrofaMutation(s): 0 
UniProt
Find proteins for P01315 (Sus scrofa)
Explore P01315 
Go to UniProtKB:  P01315
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01315
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Insulin B chain
B, D
30Sus scrofaMutation(s): 0 
UniProt
Find proteins for P01315 (Sus scrofa)
Explore P01315 
Go to UniProtKB:  P01315
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01315
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.253 (Depositor) 
  • R-Value Work:  0.209 (Depositor), 0.234 (DCC) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.225α = 90
b = 78.225β = 90
c = 36.712γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary