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- PDB-8oni: Human insulin in complex with the analytical antibody S1 Fab -

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Basic information

Entry
Database: PDB / ID: 8oni
TitleHuman insulin in complex with the analytical antibody S1 Fab
Components
  • Heavy chain of analytical antibody S1 Fab
  • Insulin A chain
  • Insulin B chain
  • Light chain of analytical antibody S1 Fab
KeywordsHORMONE / insulin / analytical antibody / S1
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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJohansson, E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Not funded Denmark
CitationJournal: To Be Published
Title: Macromolecular structure of insulin and IgE clonality impacts IgE-mediated activation of sensitized basophils
Authors: Christoffersen, S. / Baumann, K. / Millner, A.H. / Toft-Hansen, H. / Johansson, E. / Thorlaksen, C. / Skov, P.S.
History
DepositionApr 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of analytical antibody S1 Fab
L: Light chain of analytical antibody S1 Fab
C: Heavy chain of analytical antibody S1 Fab
D: Light chain of analytical antibody S1 Fab
I: Insulin A chain
B: Insulin B chain
A: Insulin A chain
F: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,68012
Polymers106,7958
Non-polymers8854
Water11,259625
1
H: Heavy chain of analytical antibody S1 Fab
L: Light chain of analytical antibody S1 Fab
I: Insulin A chain
B: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8406
Polymers53,3974
Non-polymers4422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-45 kcal/mol
Surface area21660 Å2
2
C: Heavy chain of analytical antibody S1 Fab
D: Light chain of analytical antibody S1 Fab
A: Insulin A chain
F: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8406
Polymers53,3974
Non-polymers4422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-45 kcal/mol
Surface area21390 Å2
Unit cell
Length a, b, c (Å)83.307, 71.896, 99.640
Angle α, β, γ (deg.)90.000, 112.390, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein/peptide , 2 types, 4 molecules IABF

#3: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 2
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
#4: Protein/peptide Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 2
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

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Antibody , 2 types, 4 molecules HCLD

#1: Antibody Heavy chain of analytical antibody S1 Fab


Mass: 24219.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Light chain of analytical antibody S1 Fab


Mass: 23360.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Sugars / Non-polymers , 2 types, 629 molecules

#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25%(w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→41.62 Å / Num. obs: 48254 / % possible obs: 99.17 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.05 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.06218 / Rpim(I) all: 0.03995 / Rrim(I) all: 0.07416 / Net I/σ(I): 19.81
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 3 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 6.41 / Num. unique obs: 13829 / CC1/2: 0.944 / CC star: 0.985 / Rpim(I) all: 0.1362 / Rrim(I) all: 0.2438 / % possible all: 95.74

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→41.62 Å / SU ML: 0.2587 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2375 4639 5 %
Rwork0.1974 88158 -
obs0.1995 48229 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.68 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7301 0 56 625 7982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01097548
X-RAY DIFFRACTIONf_angle_d0.732310277
X-RAY DIFFRACTIONf_chiral_restr0.0561156
X-RAY DIFFRACTIONf_plane_restr0.00551302
X-RAY DIFFRACTIONf_dihedral_angle_d5.27871050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.32721270.23392409X-RAY DIFFRACTION78.56
2.33-2.350.2951320.24442807X-RAY DIFFRACTION95.33
2.35-2.380.3211500.24372969X-RAY DIFFRACTION96.47
2.38-2.410.29331680.2262955X-RAY DIFFRACTION98.05
2.41-2.440.32251690.22832962X-RAY DIFFRACTION99.55
2.44-2.480.25071380.22222966X-RAY DIFFRACTION99.36
2.48-2.510.28671670.21483030X-RAY DIFFRACTION99.56
2.51-2.550.29211460.2182996X-RAY DIFFRACTION99.62
2.55-2.590.25161490.21993002X-RAY DIFFRACTION99.46
2.59-2.630.31421700.22042997X-RAY DIFFRACTION99.62
2.63-2.680.26761490.21533038X-RAY DIFFRACTION99.53
2.68-2.730.26481710.20752933X-RAY DIFFRACTION99.68
2.73-2.780.27961430.2193049X-RAY DIFFRACTION99.53
2.78-2.840.3021680.21412935X-RAY DIFFRACTION99.58
2.84-2.90.26521580.21013022X-RAY DIFFRACTION99.34
2.9-2.960.27781470.21072988X-RAY DIFFRACTION99.49
2.96-3.040.25441710.20682956X-RAY DIFFRACTION99.27
3.04-3.120.27791480.2093036X-RAY DIFFRACTION99
3.12-3.210.23961530.20312996X-RAY DIFFRACTION99.18
3.21-3.320.2221660.20692966X-RAY DIFFRACTION99.02
3.32-3.430.24931490.19482982X-RAY DIFFRACTION98.65
3.43-3.570.22861590.18642942X-RAY DIFFRACTION98.44
3.57-3.730.18691560.18112947X-RAY DIFFRACTION98.2
3.73-3.930.2161460.17822971X-RAY DIFFRACTION98.05
3.93-4.180.20351630.16832916X-RAY DIFFRACTION97.59
4.18-4.50.17321460.15962914X-RAY DIFFRACTION96.44
4.5-4.950.18421590.162855X-RAY DIFFRACTION95.02
4.95-5.670.19411670.17572877X-RAY DIFFRACTION96.24
5.67-7.130.2191520.2112901X-RAY DIFFRACTION96.89
7.13-41.620.22891520.20442841X-RAY DIFFRACTION93.8
Refinement TLS params.Method: refined / Origin x: 30.5053070492 Å / Origin y: 19.9207785494 Å / Origin z: 22.0888920002 Å
111213212223313233
T0.303476338336 Å20.00045171380102 Å2-0.0307422189667 Å2-0.19983392257 Å2-0.0236880626975 Å2--0.248938420742 Å2
L0.397728677567 °2-0.000740685536364 °20.0702622234892 °2-0.0738084230937 °2-0.0619825734504 °2--0.207717366265 °2
S0.0180306448491 Å °-0.0903254198116 Å °0.0422865900453 Å °0.0473682050751 Å °-0.0197537499407 Å °-0.0108740870416 Å °-0.0225286625183 Å °0.0067027270741 Å °0.00376698430679 Å °
Refinement TLS groupSelection details: all

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