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- PDB-8hsk: Insulin single mutant INS-Q -

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Basic information

Entry
Database: PDB / ID: 8hsk
TitleInsulin single mutant INS-Q
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin mutant
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 / Resolution: 1.64 Å
AuthorsRao, S.S. / Kundapura, S.V. / Kulal, A. / Ramagopal, U.A.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
CitationJournal: To Be Published
Title: Insulin single mutant INS-Q
Authors: Rao, S.S. / Kundapura, S.V. / Kulal, A. / Ramagopal, U.A.
History
DepositionDec 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0304
Polymers5,8382
Non-polymers1922
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-25 kcal/mol
Surface area3360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.380, 78.380, 78.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-101-

SO4

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Components

#1: Protein/peptide Insulin A chain / Small chain


Mass: 2383.698 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 BL21(DE3) (bacteria) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3454.027 Da / Num. of mol.: 1 / Mutation: H10Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01308
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium sulphate, 0.1M MES monohydrate, 30% w/v PEG MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.978 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.64→24.8 Å / Num. obs: 9939 / % possible obs: 99.5 % / Redundancy: 15.3 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rrim(I) all: 0.117 / Net I/σ(I): 18.8
Reflection shellResolution: 1.64→1.73 Å / % possible obs: 96.5 % / Redundancy: 13.5 % / Num. measured all: 18793 / Num. unique obs: 1387 / CC1/2: 0.858 / Rpim(I) all: 0.201 / Rrim(I) all: 0.757 / Net I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→24.798 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.409 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1648 439 4.417 %
Rwork0.1529 9499 -
all0.153 --
obs-9938 99.499 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.64→24.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms404 0 10 36 450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.013463
X-RAY DIFFRACTIONr_bond_other_d0.0010.018416
X-RAY DIFFRACTIONr_angle_refined_deg2.6321.643632
X-RAY DIFFRACTIONr_angle_other_deg1.6551.586960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.487558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83923.625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.571579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.957152
X-RAY DIFFRACTIONr_chiral_restr0.1340.256
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02540
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02116
X-RAY DIFFRACTIONr_nbd_refined0.2080.2101
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.2376
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2225
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0570.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1070.29
X-RAY DIFFRACTIONr_nbd_other0.220.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.29
X-RAY DIFFRACTIONr_mcbond_it1.4760.98220
X-RAY DIFFRACTIONr_mcbond_other1.4240.964219
X-RAY DIFFRACTIONr_mcangle_it2.3631.44276
X-RAY DIFFRACTIONr_mcangle_other2.3681.458277
X-RAY DIFFRACTIONr_scbond_it2.6971.333243
X-RAY DIFFRACTIONr_scbond_other2.5281.312236
X-RAY DIFFRACTIONr_scangle_it4.1451.905354
X-RAY DIFFRACTIONr_scangle_other3.9111.869343
X-RAY DIFFRACTIONr_lrange_it6.2613.043538
X-RAY DIFFRACTIONr_lrange_other6.2612.758533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.6830.169350.202648X-RAY DIFFRACTION93.8187
1.683-1.7290.151150.182688X-RAY DIFFRACTION100
1.729-1.7790.145300.151676X-RAY DIFFRACTION100
1.779-1.8330.152220.14641X-RAY DIFFRACTION100
1.833-1.8930.192270.156624X-RAY DIFFRACTION100
1.893-1.960.141420.156587X-RAY DIFFRACTION100
1.96-2.0340.233260.17583X-RAY DIFFRACTION100
2.034-2.1170.221200.149560X-RAY DIFFRACTION100
2.117-2.2110.145220.136546X-RAY DIFFRACTION100
2.211-2.3180.136230.135524X-RAY DIFFRACTION100
2.318-2.4440.142230.135488X-RAY DIFFRACTION100
2.444-2.5910.133200.136466X-RAY DIFFRACTION100
2.591-2.770.141250.136439X-RAY DIFFRACTION100
2.77-2.9910.137170.156405X-RAY DIFFRACTION100
2.991-3.2760.129220.157387X-RAY DIFFRACTION100
3.276-3.6610.151180.147331X-RAY DIFFRACTION100
3.661-4.2240.122140.14315X-RAY DIFFRACTION100
4.224-5.1660.225160.153261X-RAY DIFFRACTION100
5.166-7.2740.255140.198206X-RAY DIFFRACTION100
7.274-24.7980.28680.2124X-RAY DIFFRACTION96.3504
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)
10.69140.2281-0.40720.53210.13212.15760.03390.07990.05350.03280.06070.0142-0.1332-0.116-0.09460.04550.0070.01910.04770.01920.016318.341239.807432.2261
20.5294-0.3189-1.05860.69580.02412.92270.0470.01710.0406-0.0310.0559-0.0352-0.0716-0.0815-0.10290.04590.00840.00560.05430.00230.045922.42437.492826.6775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 21
2X-RAY DIFFRACTION2ALLB0 - 29

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