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- PDB-4f51: Human Insulin -

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Basic information

Entry
Database: PDB / ID: 4f51
TitleHuman Insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / pancreatic hormone
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 / negative regulation of fatty acid metabolic process / nitric oxide-cGMP-mediated signaling / 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 / negative regulation of fatty acid metabolic process / nitric oxide-cGMP-mediated signaling / 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 / regulation of protein localization to plasma membrane / positive regulation of nitric oxide mediated signal transduction / COPI-mediated anterograde transport / negative regulation of lipid catabolic 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 / transport vesicle / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / Insulin receptor recycling / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / 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 / regulation of transmembrane transporter activity / positive regulation of protein secretion / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / cognition / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / vasodilation / Golgi lumen / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.637 Å
AuthorsFavero-Retto, M.P. / Palmieri, L.C. / Lima, L.M.T.R.
CitationJournal: Eur J Pharm Biopharm / Year: 2013
Title: Structural meta-analysis of regular human insulin in pharmaceutical formulations.
Authors: Favero-Retto, M.P. / Palmieri, L.C. / Souza, T.A. / Almeida, F.C. / Lima, L.M.
History
DepositionMay 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,8378
Polymers11,6354
Non-polymers2024
Water1,802100
1
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)35,51124
Polymers34,90612
Non-polymers60512
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 area22210 Å2
ΔGint-699 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.990, 81.990, 33.750
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-232-

HOH

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Components

#1: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: UNP residues 90-110 / 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.: 2 / Fragment: UNP residues 25-54 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#3: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.88 Å3/Da / Density % sol: 34.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2 uL 0.1 M sodium phosphate, pH 5.5, 10% w/v PEG6000 + 2 uL 100 U/mL human insulin (Humulin R, lot # A 505073), cryoprotectant: mother liquor + 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.637→23.668 Å / Num. all: 10283 / Num. obs: 10283 / % possible obs: 98.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.637-1.733.10.1573453814550.15797.2
1.73-1.833.40.1135.6476114190.11397.9
1.83-1.963.60.1144.2483213560.11498.9
1.96-2.113.70.0836.8466612670.083100
2.11-2.323.60.0855.1398511080.08596.4
2.32-2.593.80.0668.5395110440.066100
2.59-2.993.80.0727.835069220.072100
2.99-3.663.90.0638.930287850.063100
3.66-5.183.90.05510.623175980.055100
5.18-23.6683.90.05210.912683290.05297.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 28.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.46 Å
Translation2.5 Å24.46 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER2.1.4phasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.637→23.668 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 4.575 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 500 4.9 %RANDOM
Rwork0.1518 ---
obs0.1547 10282 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.61 Å2 / Biso mean: 15.5482 Å2 / Biso min: 5.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.637→23.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 4 100 912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022894
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9471224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1335111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83224.04842
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28115140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.993153
X-RAY DIFFRACTIONr_chiral_restr0.1540.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021696
X-RAY DIFFRACTIONr_mcbond_it1.6171.5543
X-RAY DIFFRACTIONr_mcangle_it2.4382885
X-RAY DIFFRACTIONr_scbond_it4.0773351
X-RAY DIFFRACTIONr_scangle_it5.744.5339
X-RAY DIFFRACTIONr_rigid_bond_restr2.3233894
LS refinement shellResolution: 1.637→1.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 35 -
Rwork0.239 720 -
all-755 -
obs--97.17 %

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