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- PDB-4ewx: Human Insulin -

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Basic information

Entry
Database: PDB / ID: 4ewx
TitleHuman Insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / 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 / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / 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 / Insulin processing / regulation of protein secretion / 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 / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / Insulin receptor recycling / transport vesicle / insulin-like growth factor receptor binding / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / Regulation of insulin secretion / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / cell-cell signaling / insulin receptor signaling pathway / glucose homeostasis / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.201 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
DepositionApr 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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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
Water1,53185
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 area20350 Å2
ΔGint-305 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.960, 81.960, 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

51B-226-

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


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


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.87 Å3/Da / Density % sol: 34.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium phosphate, pH 5.5, 10% w/v PEG6000, cryoprotectant: mother liquor + 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.201→40.98 Å / Num. all: 3848 / Num. obs: 3848 / % possible obs: 89.6 % / Redundancy: 3.3 % / Rsym value: 0.053 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.201-2.323.10.1393.714424670.13973.6
2.32-2.463.30.1035.919665890.103100
2.46-2.633.30.0946.318465530.094100
2.63-2.843.20.0857.113674210.08579.7
2.84-3.113.40.0668.815934680.066100
3.11-3.483.30.0597.212593860.05989.8
3.48-4.023.10.03717.18752790.03771.9
4.02-4.923.50.02624.311093200.026100
4.92-6.963.50.02922.68522460.029100
6.96-20.493.30.02722.93931190.02786.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.27 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å20.49 Å
Translation2.5 Å20.49 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.1.4phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→40.98 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.884 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 14.695 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 290 7.5 %RANDOM
Rwork0.1542 3556 --
obs0.1605 3846 89.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.06 Å2 / Biso mean: 19.164 Å2 / Biso min: 4.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.201→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 4 85 897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02894
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9471224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4495111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.99424.04842
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23515140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.473153
X-RAY DIFFRACTIONr_chiral_restr0.090.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021696
X-RAY DIFFRACTIONr_rigid_bond_restr2.5383894
X-RAY DIFFRACTIONr_sphericity_free21.889536
X-RAY DIFFRACTIONr_sphericity_bonded5.5495936
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 13 -
Rwork0.194 178 -
all-191 -
obs--58.95 %

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