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- PDB-4gbl: Crystal structure of aspart insulin at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 4gbl
TitleCrystal structure of aspart insulin at pH 8.5
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / T3R3
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of protein metabolic process => GO:0051247 / negative regulation of acute inflammatory response / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / COPI-mediated anterograde transport / positive regulation of glycogen biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Signal attenuation / negative regulation of protein secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of nitric oxide mediated signal transduction / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / Regulation of insulin secretion / positive regulation of insulin receptor signaling pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / transport vesicle / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of brown fat cell differentiation / positive regulation of mitotic nuclear division / positive regulation of cell differentiation / regulation of transmembrane transporter activity / positive regulation of long-term synaptic potentiation / regulation of synaptic plasticity / cognition / activation of protein kinase B activity / positive regulation of cytokine production / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of nitric-oxide synthase activity / acute-phase response / negative regulation of proteolysis / hormone activity / vasodilation / insulin receptor binding / insulin receptor signaling pathway / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / wound healing / Golgi lumen / glucose metabolic process / regulation of protein localization / cell-cell signaling / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / positive regulation of protein kinase B signaling / protease binding / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / endoplasmic reticulum lumen / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of transcription, DNA-templated / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin-like / Insulin family signature. / Insulin-like superfamily / Insulin, conserved site
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLima, L.M.T.R. / Favero-Retto, M.P. / Palmieri, L.C.
CitationJournal: Biophys.Chem. / Year: 2013
Title: A T3R3 hexamer of the human insulin variant B28Asp.
Authors: Palmieri, L.C. / Favero-Retto, M.P. / Lourenco, D. / Lima, L.M.
History
DepositionJul 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Aug 22, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: entity / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_mutation / _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
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,08910
Polymers11,6714
Non-polymers4186
Water0
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)36,26830
Polymers35,01412
Non-polymers1,25418
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area21730 Å2
ΔGint-651 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.570, 78.570, 37.730
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

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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: 3451.926 Da / Num. of mol.: 2 / Fragment: UNP residues 25-54 / Source method: isolated from a natural source / Details: P28D Aspart variant / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
#3: Chemical ChemComp-CRS / M-CRESOL / M-Cresol


Mass: 108.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 1.92 Å3/Da / Density % sol: 35.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2 uL mother liquor (0.1 M Tris, pH 8.5, 1.5 M ammonium sulfate, 12% v/v glycerol) + 2 uL protein (aspart insulin 100 U/mL), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.461
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2011
RadiationMonochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.461 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.668
11K, H, -L20.332
ReflectionResolution: 2.5→39.285 Å / Num. all: 2950 / Num. obs: 2950 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rsym value: 0.172 / Net I/σ(I): 3.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.642.10.8070.88744190.80797.4
2.64-2.82.10.70518774080.70598.6
2.8-2.992.10.5851.18223840.58599
2.99-3.232.30.41.78353710.499.2
3.23-3.542.20.2722.47043250.27299.1
3.54-3.952.20.192.66623050.1998.1
3.95-4.562.20.14545622530.14598.3
4.56-5.592.20.1195.54902240.11999.6
5.59-7.912.20.1036.13851760.10398.9
7.91-25.2672.20.1134.8183850.11389.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZEH
Resolution: 2.5→39.285 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2814 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8369 / SU B: 15.325 / SU ML: 0.277 / SU Rfree: 0.0795 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 242 8.4 %RANDOM
Rwork0.1995 ---
obs0.2042 2895 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 110.86 Å2 / Biso mean: 63.3502 Å2 / Biso min: 28.16 Å2
Baniso -1Baniso -2Baniso -3
1-6.39 Å20 Å20 Å2
2--6.39 Å20 Å2
3----12.78 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 20 0 823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02839
X-RAY DIFFRACTIONr_bond_other_d0.0030.02541
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.961134
X-RAY DIFFRACTIONr_angle_other_deg1.0363.0191296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.223597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.60724.76242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9915131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.648152
X-RAY DIFFRACTIONr_chiral_restr0.1030.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02183
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 21 -
Rwork0.263 159 -
all-180 -
obs--79.65 %

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