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- PDB-5mt9: Human insulin in complex with serotonin and arginine -

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Basic information

Entry
Database: PDB / ID: 5mt9
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 NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / 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/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
ARGININE / SEROTONIN / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 7, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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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)97,41068
Polymers93,08232
Non-polymers4,32736
Water5,134285
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 area18010 Å2
ΔGint-335 kcal/mol
Surface area10910 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)36,69125
Polymers34,90612
Non-polymers1,78513
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19400 Å2
ΔGint-271 kcal/mol
Surface area11330 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)36,34123
Polymers34,90612
Non-polymers1,43511
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18650 Å2
ΔGint-272 kcal/mol
Surface area11590 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)36,56830
Polymers34,90612
Non-polymers1,66218
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 area19200 Å2
ΔGint-336 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.310, 159.310, 76.500
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

61d-102-

CL

71f-101-

ZN

81f-102-

CL

91f-203-

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, 321 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ARG / ARGININE / 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 / Serotonin


Mass: 176.215 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H12N2O / Comment: neurotransmitter*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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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: 45.5 %
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 PILATUS3 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: 1.88→46 Å / Num. obs: 57913 / % possible obs: 98.3 % / Redundancy: 5 % / CC1/2: 0.999 / Net I/σ(I): 15.1
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.6 / CC1/2: 0.69 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MSO

1mso


Resolution: 1.88→45.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 2867 5 %RANDOM
Rwork0.2035 55046 --
obs0.2068 57913 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.93 Å2 / Biso mean: 41.8276 Å2 / Biso min: 15.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---1.94 Å2
Refinement stepCycle: LAST / Resolution: 1.88→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 0 272 285 6223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196097
X-RAY DIFFRACTIONr_bond_other_d00.025204
X-RAY DIFFRACTIONr_angle_refined_deg1.85128288
X-RAY DIFFRACTIONr_angle_other_deg3.85311975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2545.014727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21723.592245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19515844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1171520
X-RAY DIFFRACTIONr_chiral_restr0.1190.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026712
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021316
X-RAY DIFFRACTIONr_mcbond_it4.0183.9783000
X-RAY DIFFRACTIONr_mcbond_other4.0173.9772999
X-RAY DIFFRACTIONr_mcangle_it5.5855.9083688
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 205 -
Rwork0.382 3683 -
all-3888 -
obs--89.65 %

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