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- PDB-6vet: Human insulin analog: [GluB10,HisA8,ArgA9,TyrB20]-DOI -

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Basic information

Entry
Database: PDB / ID: 6vet
TitleHuman insulin analog: [GluB10,HisA8,ArgA9,TyrB20]-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 / 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 ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic 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 respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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: 1.46 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: Nat.Struct.Mol.Biol. / Year: 2020
Title: A structurally minimized yet fully active insulin based on cone-snail venom insulin principles.
Authors: Xiong, X. / Menting, J.G. / Disotuar, M.M. / Smith, N.A. / Delaine, C.A. / Ghabash, G. / Agrawal, R. / Wang, X. / He, X. / Fisher, S.J. / MacRaild, C.A. / Norton, R.S. / Gajewiak, J. / ...Authors: Xiong, X. / Menting, J.G. / Disotuar, M.M. / Smith, N.A. / Delaine, C.A. / Ghabash, G. / Agrawal, R. / Wang, X. / He, X. / Fisher, S.J. / MacRaild, C.A. / Norton, R.S. / Gajewiak, J. / Forbes, B.E. / Smith, B.J. / Safavi-Hemami, H. / Olivera, B. / Lawrence, M.C. / Chou, D.H.
History
DepositionJan 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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
C: Insulin A chain
D: Insulin B chain
E: Insulin A chain
F: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)15,2366
Polymers15,2366
Non-polymers00
Water2,144119
1
A: Insulin A chain
B: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)5,0792
Polymers5,0792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-14 kcal/mol
Surface area3720 Å2
MethodPISA
2
C: Insulin A chain
D: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)5,0792
Polymers5,0792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-14 kcal/mol
Surface area3380 Å2
MethodPISA
3
E: Insulin A chain
F: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)5,0792
Polymers5,0792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-15 kcal/mol
Surface area3430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.371, 52.117, 80.499
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.: 3 / Mutation: T8H, S9R / 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.: 3 / Mutation: H10E,G20Y / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.95 Å3/Da / Density % sol: 37.02 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Well condition: 0.3 M magnesium formate plus 0.1 M TrisHCl. Protein: The insulin analog was prepared in a mixture that also contained receptor fragments: 5 mg/ml (IR310.T).Fv83-7 in 10mM ...Details: Well condition: 0.3 M magnesium formate plus 0.1 M TrisHCl. 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: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.46→43.75 Å / Num. obs: 21579 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.041 / Rrim(I) all: 0.149 / Net I/σ(I): 9.7
Reflection shellResolution: 1.46→1.48 Å / Redundancy: 12.5 % / Rmerge(I) obs: 4.47 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1000 / CC1/2: 0.38 / Rpim(I) all: 1.273 / Rrim(I) all: 4.653 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX(1.13-2998_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Editted version of 6VER

6ver


Resolution: 1.46→43.749 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.31
RfactorNum. reflection% reflection
Rfree0.2376 1999 9.38 %
Rwork0.2014 --
obs0.2049 21302 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.46→43.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 0 119 1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061077
X-RAY DIFFRACTIONf_angle_d0.611463
X-RAY DIFFRACTIONf_dihedral_angle_d14.447412
X-RAY DIFFRACTIONf_chiral_restr0.054160
X-RAY DIFFRACTIONf_plane_restr0.003187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.49610.40881300.40281255X-RAY DIFFRACTION91
1.4961-1.53660.40111370.34111331X-RAY DIFFRACTION99
1.5366-1.58180.31571450.31671384X-RAY DIFFRACTION100
1.5818-1.63290.32591390.29061349X-RAY DIFFRACTION100
1.6329-1.69120.33031420.27391375X-RAY DIFFRACTION100
1.6912-1.75890.26251430.24921370X-RAY DIFFRACTION100
1.7589-1.8390.26851400.22071358X-RAY DIFFRACTION100
1.839-1.93590.28941420.24941375X-RAY DIFFRACTION99
1.9359-2.05720.22881430.21111377X-RAY DIFFRACTION100
2.0572-2.21610.23211420.19351384X-RAY DIFFRACTION100
2.2161-2.43910.22651450.20681394X-RAY DIFFRACTION99
2.4391-2.7920.21341460.18141405X-RAY DIFFRACTION100
2.792-3.51730.25711480.17971437X-RAY DIFFRACTION100
3.5173-43.7490.18821570.16341509X-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)
15.35790.28981.58829.18095.99934.40050.1884-0.2202-0.25970.4419-0.15460.01310.67410.22350.00410.273-0.02620.0020.1681-0.00380.19867.332-9.416-5.405
27.40194.87693.21733.48792.37352.19660.0476-0.05940.4119-0.1541-0.1880.9189-0.174-0.35640.22540.2881-0.0575-0.02070.18620.00480.2921-0.2-3.722-10.206
39.54420.27453.39237.81392.51091.99460.20751.1610.0472-1.40320.0377-0.1625-0.69430.151-0.26410.49880.03920.0550.3679-0.00170.283211.749-7.305-13.217
42.8006-2.26524.01963.542-4.5028.20660.06410.290.3014-0.3525-0.1143-0.0172-0.6886-0.1481-0.08790.38330.03150.0340.208-0.00130.22665.8035.162-10.862
59.5555-4.2929-0.89523.44282.12972.1976-0.0976-0.11350.3107-0.0885-0.0707-0.24-0.3571-0.22840.05080.26480.0038-0.01740.14910.00760.1927.28213.804-22.122
68.9155-2.69755.89634.0061-3.94375.50790.30970.2711-0.0876-0.2287-0.1337-0.3445-0.09920.5862-0.20070.22980.01230.02910.1933-0.03160.263815.2337.721-26.157
75.4501-6.2339-6.00187.78857.32587.1727-0.11520.1821-0.2271-0.2612-0.05730.3537-0.1496-0.21810.22960.2321-0.0266-0.02770.1882-0.0140.21912.5178.075-27.195
88.9633-6.2079-5.84984.97074.61314.5016-0.22720.0241-0.38680.18940.06980.05570.35710.2020.03440.22940.02120.00870.15190.00290.210710.18-1.684-23.554
94.1067-1.5217-2.83723.1824-1.04553.6497-0.377-0.2057-0.50730.74640.05711.04951.537-0.26580.33030.4346-0.00530.04850.2858-0.08250.23947.834-11.371-30.478
105.11353.18164.39482.07892.8043.89590.0234-0.2221-0.33990.46660.2462-0.00890.55820.09-0.1060.34020.0542-0.04640.2082-0.01570.226711.263-12.868-34.864
115.7354-4.3099-3.23117.3192.40313.87740.5312-0.8478-0.53460.2556-0.29621.16180.661-0.35650.27260.3544-0.2049-0.01470.33760.08310.34921.099-7.564-37.252
127.7038-6.3051-2.35196.44631.24721.44180.10310.33910.1588-0.198-0.0363-0.4330.05270.41580.04140.30050.0056-0.01510.1753-0.0280.185913.758-7.41-39.748
135.2499-0.58781.47473.1372-4.09837.8539-0.2920.16170.4263-0.3270.20530.2993-0.6011-0.3224-0.0010.30550.021-0.04530.148-0.02490.22485.042.063-37.087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:12 )A1 - 12
2X-RAY DIFFRACTION2( CHAIN A AND RESID 13:20 )A13 - 20
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:7 )B1 - 7
4X-RAY DIFFRACTION4( CHAIN B AND RESID 8:22 )B8 - 22
5X-RAY DIFFRACTION5( CHAIN C AND RESID 1:12 )C1 - 12
6X-RAY DIFFRACTION6( CHAIN C AND RESID 13:20 )C13 - 20
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:7 )D1 - 7
8X-RAY DIFFRACTION8( CHAIN D AND RESID 8:22 )D8 - 22
9X-RAY DIFFRACTION9( CHAIN E AND RESID 1:6 )E1 - 6
10X-RAY DIFFRACTION10( CHAIN E AND RESID 7:12 )E7 - 12
11X-RAY DIFFRACTION11( CHAIN E AND RESID 13:20 )E13 - 20
12X-RAY DIFFRACTION12( CHAIN F AND RESID 1:7 )F1 - 7
13X-RAY DIFFRACTION13( CHAIN F AND RESID 8:22 )F8 - 22

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