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- PDB-4f1d: Human Insulin -

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Basic information

Entry
Database: PDB / ID: 4f1d
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 / 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 / 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 / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / 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 / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / 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 / endosome lumen / negative regulation of proteolysis / positive regulation of D-glucose import / positive regulation of protein secretion / Regulation of insulin secretion / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / negative regulation of protein catabolic process / regulation of synaptic plasticity / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / 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: 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 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Water1,856103
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 area20430 Å2
ΔGint-316 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.080, 82.080, 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-233-

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.: 103 / Source method: isolated from a natural source / Formula: H2O
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: 1.88 Å3/Da / Density % sol: 34.59 %
Crystal growTemperature: 291 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 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2010
RadiationMonochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.637→41.04 Å / Num. all: 9283 / Num. obs: 9283 / % possible obs: 88.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.637-1.733.10.1424.1433614210.14294.4
1.73-1.833.30.1016457513740.10195.2
1.83-1.963.50.1421.9355310050.14272.7
1.96-2.113.60.0982.8394410890.09885.8
2.11-2.323.70.05810.636069730.05885.2
2.32-2.593.80.05710.3396010460.057100
2.59-2.993.80.0658.931238190.06588.8
2.99-3.663.80.0579.627417160.05790.5
3.66-5.183.80.04214.319685130.04285.8
5.18-24.4743.90.04413.612603270.04497.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 28.94 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.47 Å
Translation2.5 Å24.47 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→41.04 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.244 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 439 4.7 %RANDOM
Rwork0.1641 ---
obs0.1666 9281 88.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 49.38 Å2 / Biso mean: 16.6255 Å2 / Biso min: 5.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.637→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 4 103 913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022894
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.9471224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0935111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12724.04842
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66315140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.219153
X-RAY DIFFRACTIONr_chiral_restr0.1960.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021696
X-RAY DIFFRACTIONr_mcbond_it1.2851.5543
X-RAY DIFFRACTIONr_mcangle_it2.1512885
X-RAY DIFFRACTIONr_scbond_it3.3663351
X-RAY DIFFRACTIONr_scangle_it5.0124.5339
LS refinement shellResolution: 1.637→1.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 39 -
Rwork0.224 742 -
all-781 -
obs--99.87 %

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