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- PDB-6ver: Human insulin analog: [GluB10,TyrB20]-DOI -

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Basic information

Entry
Database: PDB / ID: 6ver
TitleHuman insulin analog: [GluB10,TyrB20]-DOI
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: 1.047 Å
AuthorsMenting, J.G. / Chou, D.H.-C. / Lawrence, M.C. / Xiong, X.
Funding support Australia, United States, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1143546 Australia
Other private5-CDA-2018-572-A-N United States
CitationJournal: not published
Title: Mini-Ins: A minimal, bioactive insulin analog with alternative binding modes
Authors: Xiong, X. / Menting, J. / Disotaur, M. / Agrawal, R. / Delaine, C. / MacRaild, C. / Ghabash, G. / Kim, J.H. / Olivera, B. / Safavi, H. / Norton, R. / Forbes, B. / Fisher, S. / Lawrence, M.C. / Chou, D.
History
DepositionJan 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release

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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)4,9722
Polymers4,9722
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-15 kcal/mol
Surface area3610 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)26.905, 29.991, 44.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 2587.967 Da / Num. of mol.: 1 / Mutation: H10E, G20Y / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.82 Å3/Da / Density % sol: 32.43 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: Well condition: 100 mM Tri-HCl (pH 8.5) + 0.28 M magnesium formate. Protein: The insulin analog was prepared in a mixture that also contained receptor fragments: 5 mg/ml (IR310.T).Fv83-7 in ...Details: Well condition: 100 mM Tri-HCl (pH 8.5) + 0.28 M magnesium formate. Protein: The insulin analog was prepared in a mixture that also contained receptor fragments: 5 mg/ml (IR310.T).Fv83-7 in 10mM HEPES-NaOH (pH7.5) + 0.02% NaN3 plus three mol equivalents of the IR-A alphaCT peptide 704-719 plus 1.8 mol equivalents of the analog. The analog crystallized in isolation from the receptor fragments and it is not known whether the receptor fragments aided crystallization

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95364 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 1.047→44.86 Å / Num. obs: 17679 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.017 / Rrim(I) all: 0.04 / Net I/σ(I): 21.9
Reflection shellResolution: 1.047→1.06 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.857 / Num. unique obs: 836 / CC1/2: 0.735 / Rpim(I) all: 0.442 / Rrim(I) all: 0.969 / Rsym value: 0.442 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.13-2998_1692)refinement
XDSdata reduction
Aimless0.5.21data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Editted version of human insulin component of PDB entry 4OGA
Resolution: 1.047→24.933 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.25
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 1763 10 %Random selection
Rwork0.1863 ---
obs0.188 17629 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.047→24.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms335 0 0 38 373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011398
X-RAY DIFFRACTIONf_angle_d1.274550
X-RAY DIFFRACTIONf_dihedral_angle_d20.507155
X-RAY DIFFRACTIONf_chiral_restr0.08163
X-RAY DIFFRACTIONf_plane_restr0.00772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.047-1.07530.33451320.32121181X-RAY DIFFRACTION98
1.0753-1.10690.30961300.29011176X-RAY DIFFRACTION99
1.1069-1.14270.27691340.27491205X-RAY DIFFRACTION99
1.1427-1.18350.21211350.22941213X-RAY DIFFRACTION100
1.1835-1.23090.20021330.21151200X-RAY DIFFRACTION100
1.2309-1.28690.20411340.19041204X-RAY DIFFRACTION100
1.2869-1.35470.18021350.17711211X-RAY DIFFRACTION100
1.3547-1.43960.18261350.17391224X-RAY DIFFRACTION100
1.4396-1.55070.17791360.15041217X-RAY DIFFRACTION100
1.5507-1.70680.19431360.16871223X-RAY DIFFRACTION100
1.7068-1.95370.19071380.17891240X-RAY DIFFRACTION100
1.9537-2.46110.19161390.17191255X-RAY DIFFRACTION100
2.4611-24.9330.2171460.18961317X-RAY DIFFRACTION99

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