4CXL | pdb_00004cxl

Human insulin analogue (D-ProB8)-insulin


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.50 Å
  • R-Value Free:&nbsp
    0.197 (Depositor), 0.210 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.167 (Depositor), 0.180 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.168&nbsp(Depositor)&nbsp

Starting Model: experimental
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wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


This is version 1.3 of the entry. See complete&nbsphistory.&nbsp


Literature

An Insight Into Structural and Biological Relevance of the T/R Transition of the B-Chain N-Terminus in Human Insulin.

Kosinova, L.,&nbspVeverka, V.,&nbspNovotna, P.,&nbspCollinsova, M.,&nbspUrbanova, M.,&nbspMoody, N.R.,&nbspTurkenburg, J.P.,&nbspJiracek, J.,&nbspBrzozowski, A.M.,&nbspZakova, L.

(2014) Biochemistry&nbsp53: 3392

  • DOI:&nbsphttps://doi.org/10.1021/bi500073z
  • Primary Citation of Related Structures: &nbsp
    2MPG, 4CXL, 4CXN, 4CY7

  • PubMed Abstract:&nbsp

    The N-terminus of the B-chain of insulin may adopt two alternative conformations designated as the T- and R-states. Despite the recent structural insight into insulin-insulin receptor (IR) complexes, the physiological relevance of the T/R transition is still unclear. Hence, this study focused on the rational design, synthesis, and characterization of human insulin analogues structurally locked in expected R- or T-states. Sites B3, B5, and B8, capable of affecting the conformation of the N-terminus of the B-chain, were subjects of rational substitutions with amino acids with specific allowed and disallowed dihedral φ and ψ main-chain angles. α-Aminoisobutyric acid was systematically incorporated into positions B3, B5, and B8 for stabilization of the R-state, and N-methylalanine and d-proline amino acids were introduced at position B8 for stabilization of the T-state. IR affinities of the analogues were compared and correlated with their T/R transition ability and analyzed against their crystal and nuclear magnetic resonance structures. Our data revealed that (i) the T-like state is indeed important for the folding efficiency of (pro)insulin, (ii) the R-state is most probably incompatible with an active form of insulin, (iii) the R-state cannot be induced or stabilized by a single substitution at a specific site, and (iv) the B1-B8 segment is capable of folding into a variety of low-affinity T-like states. Therefore, we conclude that the active conformation of the N-terminus of the B-chain must be different from the "classical" T-state and that a substantial flexibility of the B1-B8 segment, where GlyB8 plays a key role, is a crucial prerequisite for an efficient insulin-IR interaction.


  • Organizational Affiliation:&nbsp

    Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INSULIN A CHAIN21Homo sapiensMutation(s): 0&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP01308&nbsp(Homo sapiens)
Explore&nbspP01308&nbsp
Go to UniProtKB: &nbspP01308
PHAROS: &nbspP01308
GTEx: &nbspENSG00000254647&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
INSULIN B CHAIN30Homo sapiensMutation(s): 1&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP01308&nbsp(Homo sapiens)
Explore&nbspP01308&nbsp
Go to UniProtKB: &nbspP01308
PHAROS: &nbspP01308
GTEx: &nbspENSG00000254647&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands&nbsp1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File&nbsp
C [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.50 Å
  • R-Value Free:&nbsp 0.197 (Depositor), 0.210 (DCC)&nbsp
  • R-Value Work:&nbsp 0.167 (Depositor), 0.180 (DCC)&nbsp
  • R-Value Observed:&nbsp0.168&nbsp(Depositor)&nbsp
Space Group:&nbspI 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.66α = 90
b = 78.66β = 90
c = 78.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View&nbspFull Validation Report



Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary