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- PDB-2omi: Structure of human insulin cocrystallized with protamine -

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Basic information

Entry
Database: PDB / ID: 2omi
TitleStructure of human insulin cocrystallized with protamine
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin NPH microcrystals / hormone
Function / homology
Function and homology information


Synthesis, secretion, and deacylation of Ghrelin / Signaling by Insulin receptor / Regulation of insulin secretion / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / IRS activation / Signal attenuation / Insulin receptor signalling cascade / COPI-mediated anterograde transport / Regulation of gene expression in beta cells / Insulin processing ...Synthesis, secretion, and deacylation of Ghrelin / Signaling by Insulin receptor / Regulation of insulin secretion / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / IRS activation / Signal attenuation / Insulin receptor signalling cascade / COPI-mediated anterograde transport / Regulation of gene expression in beta cells / Insulin processing / Amyloid fiber formation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Insulin receptor recycling / negative regulation of glycogen catabolic process / alpha-beta T cell activation / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / negative regulation of NAD(P)H oxidase activity / positive regulation of respiratory burst / regulation of protein secretion / positive regulation of peptide hormone secretion / negative regulation of respiratory burst involved in inflammatory response / negative regulation of blood vessel diameter / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of lipid biosynthetic process / regulation of transmembrane transporter activity / positive regulation of dendritic spine maintenance / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of lipid catabolic process / negative regulation of protein secretion / negative regulation of protein oligomerization / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / regulation of cellular amino acid metabolic process / positive regulation of glycolytic process / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / endosome lumen / regulation of synaptic plasticity / positive regulation of insulin receptor signaling pathway / cognition / neuron projection maintenance / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / positive regulation of cytokine secretion / positive regulation of mitotic nuclear division / negative regulation of acute inflammatory response / regulation of protein localization / positive regulation of cell differentiation / positive regulation of long-term synaptic potentiation / activation of protein kinase B activity / positive regulation of glucose import / positive regulation of blood vessel diameter / hormone activity / negative regulation of protein catabolic process / acute-phase response / negative regulation of proteolysis / insulin receptor signaling pathway / positive regulation of protein localization to nucleus / insulin receptor binding / positive regulation of nitric-oxide synthase activity / glucose metabolic process / cell-cell signaling / Golgi lumen / wound healing / glucose homeostasis / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / protease binding / positive regulation of cell migration / positive regulation of protein kinase B signaling / Golgi membrane / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / cellular protein metabolic process / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Insulin / Insulin-like / Insulin family / Insulin, conserved site / Insulin/IGF/Relaxin family / Insulin-like superfamily / Insulin family signature.
Insulin
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsNorrman, M. / Schluckebier, G.
CitationJournal: EUR.J.PHARM.SCI. / Year: 2007
Title: Structural characterization of insulin NPH formulations.
Authors: Norrman, M. / Hubalek, F. / Schluckebier, G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 22, 2007 / Release: Mar 27, 2007
RevisionDateData content typeGroupProviderType
1.0Mar 27, 2007Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
I: Insulin A chain
J: Insulin B chain
K: Insulin A chain
L: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,76822
Polymers34,90612
Non-polymers86210
Water1,982110
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19120 Å2
ΔGint-247 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)60.520, 61.840, 86.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 4 types, 120 molecules

#3: Chemical
ChemComp-RCO / RESORCINOL / 1,3-BENZENEDIOL / 1,3-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O2 / Resorcinol
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Zinc
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Chloride
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 46.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 50mM resorcinol, 400mM NaCl, 1.0mg/ml protamine 30mM phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.918 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 23, 2005
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.24→30 Å / Num. all: 16106 / Num. obs: 15881 / % possible obs: 98.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.1
Reflection shellResolution: 2.24→2.4 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2781 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: insulin hexamer R-conformation

Resolution: 2.24→29.1 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.878 / SU B: 6.045 / SU ML: 0.158 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26838 793 5 %RANDOM
Rwork0.19929 ---
Obs0.20276 15087 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.301 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.24→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 52 110 2511
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0220.0222471
r_bond_other_d
r_angle_refined_deg1.9411.9653346
r_angle_other_deg
r_dihedral_angle_1_deg7.4925285
r_dihedral_angle_2_deg36.83124.5120
r_dihedral_angle_3_deg1715369
r_dihedral_angle_4_deg14.14156
r_chiral_restr0.1540.2358
r_gen_planes_refined0.0090.021888
r_gen_planes_other
r_nbd_refined0.2250.21160
r_nbd_other
r_nbtor_refined0.3120.21747
r_nbtor_other
r_xyhbond_nbd_refined0.3450.2108
r_xyhbond_nbd_other
r_metal_ion_refined0.2050.26
r_metal_ion_other
r_symmetry_vdw_refined0.2210.236
r_symmetry_vdw_other
r_symmetry_hbond_refined0.2310.210
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it1.5481.51500
r_mcbond_other
r_mcangle_it2.34822333
r_scbond_it3.40731127
r_scangle_it5.1354.51013
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.24→2.296 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 53 -
Rwork0.194 1063 -
Obs--96.29 %

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