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- PDB-6ves: Human insulin analog: [GluB10,HisA8,ArgA9]-DOI -

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Basic information

Entry
Database: PDB / ID: 6ves
TitleHuman insulin analog: [GluB10,HisA8,ArgA9]-DOI
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: To Be 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
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)4,9732
Polymers4,9732
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-14 kcal/mol
Surface area3750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.059, 28.992, 46.943
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: 2490.857 Da / Num. of mol.: 1 / Mutation: T8H, S9R / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 2481.845 Da / Num. of mol.: 1 / Mutation: H10E / 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.: 25 / 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: 1.85 Å3/Da / Density % sol: 33.57 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: WELL CONDITION: 0.2 M calcium acetate, 0.1 M imidazole (pH 8) + 10% w/v PEG 8000 Protein was provided as a sample comprising 5 mg/ml (IR310.T).Fv83-7 in 10mM HEPES-NaOH (pH7.5) + 0.02% NaN3 ...Details: WELL CONDITION: 0.2 M calcium acetate, 0.1 M imidazole (pH 8) + 10% w/v PEG 8000 Protein was provided as a sample comprising 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 of the analog

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.85→46.94 Å / Num. obs: 3456 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.066 / Rrim(I) all: 0.162 / Net I/σ(I): 7.4
Reflection shellResolution: 1.85→1.91 Å / Redundancy: 6.2 % / Rmerge(I) obs: 2.365 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 290 / CC1/2: 0.405 / Rpim(I) all: 1.014 / Rrim(I) all: 2.588 / % possible all: 100

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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

4oga


Resolution: 1.85→24.667 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.43
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 344 10.12 %Random selection
Rwork0.1953 ---
obs0.1997 3400 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→24.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms344 0 0 25 369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004361
X-RAY DIFFRACTIONf_angle_d0.603490
X-RAY DIFFRACTIONf_dihedral_angle_d11.637222
X-RAY DIFFRACTIONf_chiral_restr0.03653
X-RAY DIFFRACTIONf_plane_restr0.00265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-2.33070.29471630.24491483X-RAY DIFFRACTION99
2.3307-24.6670.22351810.18071573X-RAY DIFFRACTION100
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)
17.33043.87821.75487.79453.30645.934-0.00940.72440.411-0.5007-0.09140.6026-0.3442-0.45030.07370.26080.0481-0.04990.3659-0.00730.2376-6.78963.7424-10.7941
22.262-3.26190.20068.67330.2097.07410.125-0.1091-0.1046-0.1356-0.08380.7157-0.477-0.7179-0.17120.2405-0.06620.01450.40790.02010.2813-2.884313.0139-5.3969
37.2729-0.3491-7.00787.9133-1.15577.0443-0.0705-0.15620.01880.48020.1008-0.50210.0620.24140.33330.2971-0.0251-0.05920.3198-0.0830.22250.0811-0.9506-6.4689
44.69524.66173.84167.57182.57113.7022-0.1311-0.52680.17280.35730.2556-0.37790.38760.2381-0.01830.19950.00380.02260.3742-0.09080.2377-2.71778.70853.0093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 21 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 7 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 22 )

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