5MT3

Human insulin in complex with serotonin and arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Computational and structural evidence for neurotransmitter-mediated modulation of the oligomeric states of human insulin in storage granules.

Palivec, V.Viola, C.M.Kozak, M.Ganderton, T.R.Krizkova, K.Turkenburg, J.P.Haluskova, P.Zakova, L.Jiracek, J.Jungwirth, P.Brzozowski, A.M.

(2017) J Biol Chem 292: 8342-8355

  • DOI: 10.1074/jbc.M117.775924
  • Primary Citation of Related Structures:  
    5MT3, 5MAM, 5MT9

  • PubMed Abstract: 
  • Human insulin is a pivotal protein hormone controlling metabolism, growth, and aging and whose malfunctioning underlies diabetes, some cancers, and neurodegeneration. Despite its central position in human physiology, the in vivo oligomeric state ...

    Human insulin is a pivotal protein hormone controlling metabolism, growth, and aging and whose malfunctioning underlies diabetes, some cancers, and neurodegeneration. Despite its central position in human physiology, the in vivo oligomeric state and conformation of insulin in its storage granules in the pancreas are not known. In contrast, many in vitro structures of hexamers of this hormone are available and fall into three conformational states: T 6 , T 3 R f 3 , and R 6 As there is strong evidence for accumulation of neurotransmitters, such as serotonin and dopamine, in insulin storage granules in pancreatic β-cells, we probed by molecular dynamics (MD) and protein crystallography (PC) if these endogenous ligands affect and stabilize insulin oligomers. Parallel studies independently converged on the observation that serotonin binds well within the insulin hexamer (site I), stabilizing it in the T 3 R 3 conformation. Both methods indicated serotonin binding on the hexamer surface (site III) as well. MD, but not PC, indicated that dopamine was also a good site III ligand. Some of the PC studies also included arginine, which may be abundant in insulin granules upon processing of pro-insulin, and stable T 3 R 3 hexamers loaded with both serotonin and arginine were obtained. The MD and PC results were supported further by in solution spectroscopic studies with R-state-specific chromophore. Our results indicate that the T 3 R 3 oligomer is a plausible insulin pancreatic storage form, resulting from its complex interplay with neurotransmitters, and pro-insulin processing products. These findings may have implications for clinical insulin formulations.


    Organizational Affiliation

    From the York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom and marek.brzozowski@york.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
InsulinACEGIKMOACEGIKMOQSUWYace
21Homo sapiensMutation(s): 0 
Gene Names: INS
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
InsulinBDFHJLNPBDFHJLNPRTVXZbdf
30Homo sapiensMutation(s): 0 
Gene Names: INS
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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRO
Query on SRO

Download Ideal Coordinates CCD File 
C, E, G, I, K, O, Q, S, W, a, c, d
SEROTONIN
C10 H12 N2 O
QZAYGJVTTNCVMB-UHFFFAOYSA-N
 Ligand Interaction
ARG
Query on ARG

Download Ideal Coordinates CCD File 
B, F, L, N
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B, D, E, F, H, T, d, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B, D, F, H, T, f
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SROKd:  3120000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.240 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.64α = 90
b = 158.64β = 90
c = 76.1γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references