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- PDB-4iyd: Insulin glargine crystal structure 1 -

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Basic information

Entry
Database: PDB / ID: 4iyd
TitleInsulin glargine crystal structure 1
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 / 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 / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / 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 / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / 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 / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsBarba de la Rosa, A.P. / Lara-Gonzalez, S. / Montero-Moran, G.M. / Escobedo-Moratilla, A.
CitationJournal: to be published
Title: Physicochemical and structural analysis of a biosimilar insulin glargine formulation and its reference
Authors: Barba de la Rosa, A.P. / Lara-Gonzalez, S. / Montero-Moran, G.M. / Escobedo-Moratilla, A. / Perez-Urizar, J.T.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)5,6592
Polymers5,6592
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-14 kcal/mol
Surface area3280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.325, 77.325, 77.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein/peptide Insulin A chain


Mass: 2326.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3332.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P01308
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, 30% PEG-400 v/v, 0.2 M sodium citrate dihydrate, pH 8.0, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 1.66→31.57 Å / Num. obs: 9252 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.29 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.067 / Χ2: 0.95 / Net I/σ(I): 11.1 / Scaling rejects: 301
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.66-1.724.190.454239019300.53100
1.72-1.794.220.3532.737858970.6100
1.79-1.874.250.2723.738669090.67100
1.87-1.974.280.234.939779280.83100
1.97-2.094.340.1756.739939190.85100
2.09-2.254.350.1358.739349040.8499.9
2.25-2.484.410.11110.641279360.8100
2.48-2.844.40.09213.640419170.85100
2.84-3.584.370.07121.841619391.3199.8
3.58-31.574.050.06135.441669732.2699.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.6 W9RSSIdata reduction
PHASER2.5.3phasing
PHENIXdev_1184refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1trz

1trz


Resolution: 1.66→31.568 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.15 / Isotropic thermal model: ISOTROPIC / σ(F): 1.4 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 915 9.89 %RANDOM
Rwork0.1969 ---
all0.1995 9250 --
obs-9250 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.8 Å2 / Biso mean: 36.1302 Å2 / Biso min: 22.01 Å2
Refinement stepCycle: LAST / Resolution: 1.66→31.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms379 0 0 11 390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016389
X-RAY DIFFRACTIONf_angle_d1.37523
X-RAY DIFFRACTIONf_chiral_restr0.09459
X-RAY DIFFRACTIONf_plane_restr0.00967
X-RAY DIFFRACTIONf_dihedral_angle_d13.41130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.66-1.74820.29681300.247117613061176
1.7482-1.85780.2621290.2298118713161187
1.8578-2.00120.25991280.2216117213001172
2.0012-2.20250.2241350.1985117113061171
2.2025-2.52110.20171310.1965118313141183
2.5211-3.17590.25871300.2002120513351205
3.1759-31.57340.2051320.1868124113731241
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2448-0.12120.30290.205-0.13570.3483-0.0795-0.3195-0.37670.2590.2008-0.13670.21790.3293-0.00040.32620.0458-0.01740.4054-0.01530.4122-4.8684-19.23473.1234
20.11340.016-0.1410.2471-0.08040.1813-0.45740.1801-0.7974-0.11360.1597-0.49130.72890.7001-0.00650.33030.04760.04530.29560.00320.3159-9.6492-23.9749-3.8626
30.0640.04510.04890.153-0.02170.0495-0.21650.63490.8687-0.3770.3224-0.3763-0.41720.3277-0.00080.3511-0.0143-0.01510.5290.01440.3497-6.0517-11.840.2859
40.2808-0.00060.00490.0691-0.10490.15-0.1672-0.37910.44530.15430.1924-0.3228-0.5795-0.07610.00010.25340.04590.02240.3015-0.02190.2789-14.9229-13.6973-0.3997
50.74010.01260.44130.1370.08140.67340.20510.26-0.42080.02910.0882-0.11720.4287-0.09230.01410.289-0.00140.01750.3013-0.03020.2277-16.1235-20.5556-7.935
60.0595-0.0007-0.0290.044-0.00130.0466-0.10890.2124-0.80210.62190.4558-1.04580.17630.2502-0.00340.39440.0699-0.01840.42870.05010.3446-15.3215-22.93775.9176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)A1 - 14
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:21)A15 - 21
3X-RAY DIFFRACTION3(CHAIN B AND RESID 1:7)B1 - 7
4X-RAY DIFFRACTION4(CHAIN B AND RESID 8:16)B8 - 16
5X-RAY DIFFRACTION5(CHAIN B AND RESID 17:24)B17 - 24
6X-RAY DIFFRACTION6(CHAIN B AND RESID 25:29)B25 - 29

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