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- PDB-5mt3: Human insulin in complex with serotonin and arginine -

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Basic information

Entry
Database: PDB / ID: 5mt3
TitleHuman insulin in complex with serotonin and arginine
Components(Insulin) x 2
KeywordsHORMONE / serotonin / arginine / complex / specificity
Function / homology
Function and homology information


negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of cytokine production / positive regulation of glycolytic process / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / Regulation of insulin secretion / positive regulation of cell differentiation / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
ARGININE / SEROTONIN / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsBrzozowski, A.M. / Turkenburg, J.P. / Jiracek, J. / Zakova, L.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Computational and structural evidence for neurotransmitter-mediated modulation of the oligomeric states of human insulin in storage granules.
Authors: 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.
History
DepositionJan 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin
B: Insulin
C: Insulin
D: Insulin
E: Insulin
F: Insulin
G: Insulin
H: Insulin
I: Insulin
J: Insulin
K: Insulin
L: Insulin
M: Insulin
N: Insulin
O: Insulin
P: Insulin
Q: Insulin
R: Insulin
S: Insulin
T: Insulin
U: Insulin
V: Insulin
W: Insulin
X: Insulin
Y: Insulin
Z: Insulin
a: Insulin
b: Insulin
c: Insulin
d: Insulin
e: Insulin
f: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,63462
Polymers93,08232
Non-polymers3,55130
Water5,260292
1
A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules

A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules

A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,56530
Polymers34,90612
Non-polymers1,65918
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17560 Å2
ΔGint-330 kcal/mol
Surface area9990 Å2
MethodPISA
2
E: Insulin
F: Insulin
G: Insulin
H: Insulin
I: Insulin
J: Insulin
K: Insulin
L: Insulin
M: Insulin
N: Insulin
O: Insulin
P: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,58025
Polymers34,90612
Non-polymers1,67413
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19330 Å2
ΔGint-263 kcal/mol
Surface area11260 Å2
MethodPISA
3
Q: Insulin
R: Insulin
S: Insulin
T: Insulin
U: Insulin
V: Insulin
W: Insulin
X: Insulin
Y: Insulin
Z: Insulin
a: Insulin
b: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,71218
Polymers34,90612
Non-polymers8066
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17930 Å2
ΔGint-254 kcal/mol
Surface area12000 Å2
MethodPISA
4
c: Insulin
d: Insulin
e: Insulin
f: Insulin
hetero molecules

c: Insulin
d: Insulin
e: Insulin
f: Insulin
hetero molecules

c: Insulin
d: Insulin
e: Insulin
f: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,46227
Polymers34,90612
Non-polymers1,55615
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19140 Å2
ΔGint-310 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.640, 158.640, 76.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-101-

ZN

21B-102-

CL

31D-101-

ZN

41D-102-

CL

51d-101-

ZN

61f-101-

ZN

71f-102-

CL

81D-201-

HOH

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Components

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Protein/peptide , 2 types, 32 molecules ACEGIKMOQSUWYaceBDFHJLNPRTVXZbdf

#1: Protein/peptide
Insulin


Mass: 2383.698 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin


Mass: 3433.953 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 5 types, 322 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N4O2
#6: Chemical
ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H12N2O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5 mM ZnAcetate, 35 mM NaCitrate, 1.1 M NaCl, 0.3M Tris pH 7.5, 40 mM serotonin, 100 mM arginine.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→42.9 Å / Num. obs: 46018 / % possible obs: 98.3 % / Redundancy: 4.9 % / CC1/2: 0.998 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.6 / CC1/2: 0.758 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MSO

1mso


Resolution: 2.02→42.89 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.241
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3099 2266 4.9 %RANDOM
Rwork0.2362 ---
obs0.24 46012 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.7 Å2 / Biso mean: 42.855 Å2 / Biso min: 14.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0.29 Å20 Å2
2---0.58 Å20 Å2
3---1.9 Å2
Refinement stepCycle: LAST / Resolution: 2.02→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5665 0 218 292 6175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196070
X-RAY DIFFRACTIONr_bond_other_d00.025091
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9948252
X-RAY DIFFRACTIONr_angle_other_deg3.935311735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9555731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87623.603247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58315829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2621518
X-RAY DIFFRACTIONr_chiral_restr0.1030.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026808
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021313
X-RAY DIFFRACTIONr_mcbond_it3.5714.1733017
X-RAY DIFFRACTIONr_mcbond_other3.5694.1723016
X-RAY DIFFRACTIONr_mcangle_it5.1776.1993716
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 154 -
Rwork0.372 3216 -
all-3370 -
obs--97.77 %

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