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- PDB-8pi5: Crystal structure of human insulin desB30 precursor with an Alani... -

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Basic information

Entry
Database: PDB / ID: 8pi5
TitleCrystal structure of human insulin desB30 precursor with an Alanine-Methionine-Lysine C-peptide in hexamer (T3R3) conformation
ComponentsInsulin B chain,Insulin A chain
KeywordsHORMONE / insulin / precursor / dimer
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 / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / positive regulation of insulin receptor signaling pathway / negative regulation of respiratory burst involved in inflammatory response / 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 / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / 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 glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import across plasma membrane / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / regulation of synaptic plasticity / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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
RESORCINOL / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Insulin B chain,Insulin A chain
D: Insulin B chain,Insulin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4678
Polymers12,0602
Non-polymers4076
Water1,69394
1
B: Insulin B chain,Insulin A chain
D: Insulin B chain,Insulin A chain
hetero molecules

B: Insulin B chain,Insulin A chain
D: Insulin B chain,Insulin A chain
hetero molecules

B: Insulin B chain,Insulin A chain
D: Insulin B chain,Insulin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,40224
Polymers36,1806
Non-polymers1,22218
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Unit cell
Length a, b, c (Å)79.353, 79.353, 39.185
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11B-101-

ZN

21B-102-

ZN

31B-103-

ZN

41D-101-

ZN

51D-102-

CL

61B-235-

HOH

71B-242-

HOH

81D-242-

HOH

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Components

#1: Protein Insulin B chain,Insulin A chain


Mass: 6029.985 Da / Num. of mol.: 2
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: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-RCO / RESORCINOL / 1,3-BENZENEDIOL / 1,3-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.97 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 6 mg/ml protein, 20 mM resorcinol, 0.5 Zn2+ (from zinc acetate) per insuln monomer in water, pH 7.95 precipitant: 0.1 M Bicine, pH 9.0, 2 % (v/v) 1,4-dioxane, 10 % (w/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.66→13.66 Å / Num. obs: 10563 / % possible obs: 97.17 % / Redundancy: 6.1 % / Biso Wilson estimate: 21.26 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04731 / Rpim(I) all: 0.01975 / Rrim(I) all: 0.05135 / Net I/σ(I): 25.54
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3121 / Mean I/σ(I) obs: 3.58 / Num. unique obs: 829 / CC1/2: 0.847 / CC star: 0.958 / Rpim(I) all: 0.2031 / Rrim(I) all: 0.375 / % possible all: 76.19

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→13.66 Å / SU ML: 0.1539 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.8241
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1786 1020 4.99 %
Rwork0.1536 19405 -
obs0.1549 10558 94.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.36 Å2
Refinement stepCycle: LAST / Resolution: 1.66→13.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 13 94 945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081894
X-RAY DIFFRACTIONf_angle_d0.87371215
X-RAY DIFFRACTIONf_chiral_restr0.0448132
X-RAY DIFFRACTIONf_plane_restr0.0057158
X-RAY DIFFRACTIONf_dihedral_angle_d14.313316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.750.26671030.24821936X-RAY DIFFRACTION65.44
1.75-1.860.26651480.21452784X-RAY DIFFRACTION94.58
1.86-20.20171540.17372939X-RAY DIFFRACTION99.65
2-2.20.17761560.16372932X-RAY DIFFRACTION99.94
2.2-2.520.16251480.16822931X-RAY DIFFRACTION99.97
2.52-3.160.15081580.15372949X-RAY DIFFRACTION99.97
3.17-13.660.17771530.12592934X-RAY DIFFRACTION99.64

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