6X4X

B24Y DKP insulin

  • Classification: HORMONE
  • Organism(s): Homo sapiens
  • Expression System: Komagataella pastoris
  • Mutation(s): Yes 

  • Deposited: 2020-05-24 Released: 2020-08-05 
  • Deposition Author(s): Weiss, M.A., Yang, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Evolution of insulin at the edge of foldability and its medical implications.

Rege, N.K., Liu, M., Yang, Y., Dhayalan, B., Wickramasinghe, N.P., Chen, Y.S., Rahimi, L., Guo, H., Haataja, L., Sun, J., Ismail-Beigi, F., Phillips, N.B., Arvan, P., Weiss, M.A.

(2020) Proc Natl Acad Sci U S A 117: 29618-29628

  • DOI: 10.1073/pnas.2010908117
  • Primary Citation of Related Structures:  
    6X4X

  • PubMed Abstract: 

    • Proteins have evolved to be foldable, and yet determinants of foldability may be inapparent once the native state is reached. Insight has emerged from studies of diseases of protein misfolding, exemplified by monogenic diabetes mellitus due to mutations in proinsulin leading to endoplasmic reticulum stress and β-cell death ...

    Proteins have evolved to be foldable, and yet determinants of foldability may be inapparent once the native state is reached. Insight has emerged from studies of diseases of protein misfolding, exemplified by monogenic diabetes mellitus due to mutations in proinsulin leading to endoplasmic reticulum stress and β-cell death. Cellular foldability of human proinsulin requires an invariant Phe within a conserved crevice at the receptor-binding surface (position B24). Any substitution, even related aromatic residue Tyr B24 , impairs insulin biosynthesis and secretion. As a seeming paradox, a monomeric Tyr B24 insulin analog exhibits a native-like structure in solution with only a modest decrement in stability. Packing of Tyr B24 is similar to that of Phe B24 , adjoining core cystine B19-A20 to seal the core; the analog also exhibits native self-assembly. Although affinity for the insulin receptor is decreased ∼20-fold, biological activities in cells and rats were within the range of natural variation. Together, our findings suggest that the invariance of Phe B24 among vertebrate insulins and insulin-like growth factors reflects an essential role in enabling efficient protein folding, trafficking, and secretion, a function that is inapparent in native structures. In particular, we envision that the para -hydroxyl group of Tyr B24 hinders pairing of cystine B19-A20 in an obligatory on-pathway folding intermediate. The absence of genetic variation at B24 and other conserved sites near this disulfide bridge-excluded due to β-cell dysfunction-suggests that insulin has evolved to the edge of foldability. Nonrobustness of a protein's fitness landscape underlies both a rare monogenic syndrome and "diabesity" as a pandemic disease of civilization.

    Organizational Affiliation: 

    Department of Medicine, Case Western Reserve University, Cleveland, OH 44106.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin chain AA21Homo sapiensMutation(s): 0 
Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
Entity Groups  
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UniProt GroupP01308
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
InsulinB30Homo sapiensMutation(s): 4 
Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 
  • OLDERADO: 6X4X Olderado

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-05-24 
  • Released Date: 2020-08-05 
    • Deposition Author(s): Weiss, M.A., Yang, Y.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2020-12-09
    Changes: Database references