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- PDB-8pi6: Crystal structure of the monomeric zinc free human insulin A22K, ... -

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Basic information

Entry
Database: PDB / ID: 8pi6
TitleCrystal structure of the monomeric zinc free human insulin A22K, B3E, B26E, B29R, desB30 precursor with a Ser-Glu-Asp-Trp-Trp-Arg C-peptide and a Glu-Glu-Gly-Glu-Pro-Arg N-terminal extension
ComponentsInsulin B chain,Insulin A chain
KeywordsHORMONE / insulin / precursor / dimer
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 / 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 / Insulin processing / 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 / 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 / Insulin processing / regulation of protein secretion / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsJohansson, E. / Schluckebier, G.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Not funded Denmark
CitationJournal: Trends Biotechnol / Year: 2024
Title: Molecular engineering of insulin for recombinant expression in yeast.
Authors: Kjeldsen, T. / Andersen, A.S. / Hubalek, F. / Johansson, E. / Kreiner, F.F. / Schluckebier, G. / Kurtzhals, P.
History
DepositionJun 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin B chain,Insulin A chain
B: Insulin B chain,Insulin A chain
C: Insulin B chain,Insulin A chain
D: Insulin B chain,Insulin A chain
E: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)36,9815
Polymers36,9815
Non-polymers00
Water28816
1
A: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.240, 60.020, 90.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Insulin B chain,Insulin A chain


Mass: 7396.271 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.95 Å3/Da / Density % sol: 37.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 8 mg/ml protein in water precipitant: 0.1 M sodium citrate, pH 5.6, 1.o M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.075 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.075 Å / Relative weight: 1
ReflectionResolution: 2.14→45.88 Å / Num. obs: 14677 / % possible obs: 84.68 % / Redundancy: 109.8 % / Biso Wilson estimate: 41.94 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.01512 / Rrim(I) all: 0.1727 / Net I/σ(I): 33.01
Reflection shellResolution: 2.14→2.219 Å / Redundancy: 16.1 % / Rmerge(I) obs: 2.496 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 726 / CC1/2: 0.0712 / CC star: 0.365 / Rpim(I) all: 0.5138 / Rrim(I) all: 2.562 / % possible all: 44.84

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→45.88 Å / SU ML: 0.2676 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 34.4413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2878 1390 9.94 %
Rwork0.2378 12594 -
obs0.243 13984 84.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.09 Å2
Refinement stepCycle: LAST / Resolution: 2.14→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 0 16 2302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182357
X-RAY DIFFRACTIONf_angle_d0.52013193
X-RAY DIFFRACTIONf_chiral_restr0.0323327
X-RAY DIFFRACTIONf_plane_restr0.0025414
X-RAY DIFFRACTIONf_dihedral_angle_d3.7551311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.220.3867700.4513656X-RAY DIFFRACTION44.87
2.22-2.310.39251010.3594908X-RAY DIFFRACTION62.55
2.31-2.410.3741270.32451141X-RAY DIFFRACTION77.98
2.41-2.540.31751380.28111231X-RAY DIFFRACTION84.45
2.54-2.70.32341470.2811311X-RAY DIFFRACTION89.67
2.7-2.910.3821440.30271367X-RAY DIFFRACTION92.3
2.91-3.20.30441570.26581419X-RAY DIFFRACTION95.75
3.2-3.660.30111630.23991470X-RAY DIFFRACTION98.08
3.66-4.610.27361650.19671497X-RAY DIFFRACTION98.93
4.61-45.880.2361780.19941594X-RAY DIFFRACTION99.66
Refinement TLS params.Method: refined / Origin x: 60.4524471165 Å / Origin y: 65.770051835 Å / Origin z: 82.5634760152 Å
111213212223313233
T0.22385873665 Å2-0.0181292366532 Å2-0.0312291707996 Å2-0.32357026202 Å2-0.0156804799795 Å2--0.129379031979 Å2
L0.588678353765 °2-0.224359917688 °2-0.331966836156 °2-0.82213179722 °2-0.330423659663 °2--0.996888283131 °2
S-0.00940211826019 Å °-0.0269265768922 Å °-0.0421415122721 Å °0.0629819483566 Å °-0.0274519272117 Å °0.0257553097211 Å °0.223313349123 Å °-0.0659990416274 Å °0.0237832339152 Å °
Refinement TLS groupSelection details: all

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