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- PDB-4nib: Crystal structure of human insulin mutant B20 D-ala, B23 D-ala -

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Basic information

Entry
Database: PDB / ID: 4nib
TitleCrystal structure of human insulin mutant B20 D-ala, B23 D-ala
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / negative regulation of reactive oxygen species biosynthetic process / positive regulation of cellular protein metabolic process / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / Regulation of insulin secretion / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / regulation of cellular amino acid metabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / fatty acid homeostasis / endosome lumen / transport vesicle / positive regulation of insulin receptor signaling pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / negative regulation of acute inflammatory response / regulation of transmembrane transporter activity / positive regulation of cell differentiation / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / regulation of synaptic plasticity / positive regulation of brown fat cell differentiation / cognition / regulation of protein localization / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / vasodilation / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / insulin receptor signaling pathway / glucose metabolic process / Golgi lumen / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / wound healing / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of MAPK cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell migration / positive regulation of protein kinase B signaling / Amyloid fiber formation / Golgi membrane / G protein-coupled receptor signaling pathway / amyloid fibril formation / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin-like superfamily / Insulin family signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMenting, J.G. / Lawrence, M.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Protective hinge in insulin opens to enable its receptor engagement.
Authors: Menting, J.G. / Yang, Y. / Chan, S.J. / Phillips, N.B. / Smith, B.J. / Whittaker, J. / Wickramasinghe, N.P. / Whittaker, L.J. / Pandyarajan, V. / Wan, Z.L. / Yadav, S.P. / Carroll, J.M. / ...Authors: Menting, J.G. / Yang, Y. / Chan, S.J. / Phillips, N.B. / Smith, B.J. / Whittaker, J. / Wickramasinghe, N.P. / Whittaker, L.J. / Pandyarajan, V. / Wan, Z.L. / Yadav, S.P. / Carroll, J.M. / Strokes, N. / Roberts, C.T. / Ismail-Beigi, F. / Milewski, W. / Steiner, D.F. / Chauhan, V.S. / Ward, C.W. / Weiss, M.A. / Lawrence, M.C.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2May 6, 2015Group: Structure summary

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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)5,8462
Polymers5,8462
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-15 kcal/mol
Surface area3400 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)78.030, 78.030, 78.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-125-

HOH

21B-112-

HOH

31B-127-

HOH

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Components

#1: Protein/peptide Insulin A chain / Insulin


Mass: 2383.698 Da / Num. of mol.: 1 / Mutation: G20(DAL), G23(DAL) / Source method: obtained synthetically / Details: Laboratory synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain / Insulin


Mass: 3462.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Laboratory synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: These insulin crystals were obtained from a co-crystallization experiment with insulin receptor fragment IR310.T. Crystals were formed in the presence of IR310.T as detailed for the IR310.T ...Details: These insulin crystals were obtained from a co-crystallization experiment with insulin receptor fragment IR310.T. Crystals were formed in the presence of IR310.T as detailed for the IR310.T complex with native human insulin - in Menting et al. 2013, Nature 493:241-245. Crystallant was 0.7 M trisodium citrate, 0.1 M imidazole-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2013
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 19350 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.66 / Redundancy: 11.5 %
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.3-1.357.20.551852189.1
1.35-1.411.60.9917751100
1.4-1.512.11.7129081100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B2A
Resolution: 1.4→18.392 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0.53 / Phase error: 15.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.163 1568 9.97 %random
Rwork0.1411 ---
obs0.1433 15723 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→18.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms407 0 0 83 490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009418
X-RAY DIFFRACTIONf_angle_d1.073563
X-RAY DIFFRACTIONf_dihedral_angle_d12.858144
X-RAY DIFFRACTIONf_chiral_restr0.07664
X-RAY DIFFRACTIONf_plane_restr0.00572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4001-1.44530.28841400.235112791279100
1.4453-1.49690.25561420.19912691269100
1.4969-1.55680.22891380.171112771277100
1.5568-1.62760.20981370.155512591259100
1.6276-1.71340.16391430.13312711271100
1.7134-1.82060.13131460.116712941294100
1.8206-1.96110.17251460.1212821282100
1.9611-2.15810.15881390.113212871287100
2.1581-2.46980.13091420.124812821282100
2.4698-3.10920.15911470.145913111311100
3.1092-18.39340.15581480.14691343134399

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