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- PDB-8pi4: Crystal structure of human insulin desB30 precursor with an Alani... -

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Basic information

Entry
Database: PDB / ID: 8pi4
TitleCrystal structure of human insulin desB30 precursor with an Alanine-Methionine-Lysine C-peptide in dimer (T2) conformation
ComponentsInsulin B chain,Insulin A chain
KeywordsHORMONE / insulin / precursor / dimer
Function / homology
Function and homology information


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 / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...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 / regulation of protein secretion / Insulin processing / 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 / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / 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-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: 1.25 Å
AuthorsJohansson, E. / Schluckebier, G.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Not funded Denmark
CitationJournal: Trends Biotechnol / Year: 2024
Title: Molecular engineering of insulin for recombinant expression in yeast.
Authors: Kjeldsen, T. / Andersen, A.S. / Hubalek, F. / Johansson, E. / Kreiner, F.F. / Schluckebier, G. / Kurtzhals, P.
History
DepositionJun 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.entity_id_list
Revision 1.2Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)6,0301
Polymers6,0301
Non-polymers00
Water90150
1
A: Insulin B chain,Insulin A chain

A: Insulin B chain,Insulin A chain


Theoretical massNumber of molelcules
Total (without water)12,0602
Polymers12,0602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
point symmetry operation1
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.400, 77.400, 77.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11A-128-

HOH

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Components

#1: Protein Insulin B chain,Insulin A chain


Mass: 6029.985 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.2 Å3/Da / Density % sol: 61.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris, pH 8.5, 30 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→38.7 Å / Num. obs: 21467 / % possible obs: 99.99 % / Redundancy: 19.7 % / Biso Wilson estimate: 20.02 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05152 / Rpim(I) all: 0.01181 / Rrim(I) all: 0.05288 / Net I/σ(I): 25.55
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 19.8 % / Rmerge(I) obs: 1.391 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 2099 / CC1/2: 0.77 / CC star: 0.933 / Rpim(I) all: 0.3203 / Rrim(I) all: 1.428 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→38.7 Å / SU ML: 0.1024 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1755 1074 5 %
Rwork0.1732 20393 -
obs0.1733 21467 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.73 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms419 0 0 50 469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098451
X-RAY DIFFRACTIONf_angle_d1.0634615
X-RAY DIFFRACTIONf_chiral_restr0.085168
X-RAY DIFFRACTIONf_plane_restr0.006980
X-RAY DIFFRACTIONf_dihedral_angle_d6.953264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.310.28761310.28822547X-RAY DIFFRACTION100
1.31-1.380.23981280.23262490X-RAY DIFFRACTION100
1.38-1.460.21481340.22372542X-RAY DIFFRACTION100
1.46-1.570.23361310.19262500X-RAY DIFFRACTION100
1.58-1.730.20831320.19982575X-RAY DIFFRACTION100
1.73-1.980.1711390.18892541X-RAY DIFFRACTION100
1.99-2.50.17061370.16592555X-RAY DIFFRACTION100
2.5-38.70.16151420.15842643X-RAY DIFFRACTION99.96
Refinement TLS params.Method: refined / Origin x: -18.7071325239 Å / Origin y: 0.316354109453 Å / Origin z: -10.1490809227 Å
111213212223313233
T0.191403560646 Å20.0204859017361 Å20.0240442653573 Å2-0.175253841343 Å20.0243300053635 Å2--0.143294089573 Å2
L2.24758036831 °2-0.00178114699872 °2-0.435175242797 °2-2.8837625392 °20.520650816717 °2--4.30182067809 °2
S0.0447186936169 Å °-0.0385109457877 Å °0.0980288710188 Å °0.16541086609 Å °0.0143648038082 Å °0.124841929962 Å °-0.156082799288 Å °-0.213184470122 Å °-0.0519863519768 Å °
Refinement TLS groupSelection details: all

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