3GKY

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 
  • R-Value Work: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 Biol Chem 284: 35259-35272

  • DOI: 10.1074/jbc.M109.046888
  • Primary Citation of 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 ...

    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.


    Related Citations: 
    • The structure of 2zn pig insulin crystal at 1.5 A resolution
      Baker, E.N., Blujdell, T.L., Cutfield, J.F., Cutfield, S.M., Dodson, E.J., Dodson, G.G., Hodgkin, D., Isaacs, N.W., Reynolds, C.D.
      (1988) Philos Trans R Soc London,ser B 319: 369
    • Structure of insulin in 4-zinc insulin
      Bentley, G., Dodson, E., Dodson, G., Hodgkin, D., Mercola, D.
      (1976) Nature 261: 166
    • Phenol stabilizes more helix in a new symmetrical zinc insulin hexamer
      Derewenda, U., Derewenda, Z., Dodson, E., Dodson, G., Reynold, C., Smith, G., Sparks, C., Swenson, D.
      (1989) Nature 338: 594
    • Toward the active conformation of insulin: stereospecific modulation of a structural swith in the B chain
      Hua, Q.X., Nakagawa, S., Hu, S.Q., Jia, W., Wang, S., Weiss, M.A.
      (2006) J Biol Chem 281: 24900

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin A chainA, C21Sus scrofaMutation(s): 0 
Gene Names: INS
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin B chainB, D30Sus scrofaMutation(s): 0 
Gene Names: INS
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPH
Query on IPH

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

Download Ideal Coordinates CCD File 
E [auth B],
H [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth B],
I [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.209 
  • 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

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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