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 

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Ligand Structure Quality Assessment 


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:  
    5MAM, 5MT3, 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 and conformation of insulin in its storage granules in the pancreas are not known ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin
A,
C,
E,
G,
I,
21Homo 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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
Insulin
B,
D,
F,
H,
J,
30Homo 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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRO
Query on SRO

Download Ideal Coordinates CCD File 
AB [auth S],
DB [auth W],
EB [auth a],
FB [auth c],
HB [auth d],
AB [auth S],
DB [auth W],
EB [auth a],
FB [auth c],
HB [auth d],
JA [auth C],
NA [auth E],
RA [auth G],
UA [auth I],
VA [auth K],
YA [auth O],
ZA [auth Q]
SEROTONIN
C10 H12 N2 O
QZAYGJVTTNCVMB-UHFFFAOYSA-N
 Ligand Interaction
ARG
Query on ARG

Download Ideal Coordinates CCD File 
IA [auth B],
QA [auth F],
WA [auth L],
XA [auth N]
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BB [auth T],
GA [auth B],
GB [auth d],
IB [auth f],
KA [auth D],
BB [auth T],
GA [auth B],
GB [auth d],
IB [auth f],
KA [auth D],
MA [auth E],
OA [auth F],
SA [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
CB [auth T],
HA [auth B],
JB [auth f],
LA [auth D],
PA [auth F],
CB [auth T],
HA [auth B],
JB [auth f],
LA [auth D],
PA [auth F],
TA [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SRO Binding MOAD:  5MT3 Kd: 3.12e+6 (nM) from 1 assay(s)
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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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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