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- PDB-9lvy: hexamer form of insulin detemir at ambient temperature -

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Basic information

Entry
Database: PDB / ID: 9lvy
Titlehexamer form of insulin detemir at ambient temperature
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin structure / insulin hexamer / ambient temperature
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of protein autophosphorylation / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / regulation of transmembrane transporter activity / 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 / negative regulation of protein secretion / activation of protein kinase B activity / positive regulation of insulin receptor signaling pathway / negative regulation of gluconeogenesis / 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 / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / transport vesicle / nitric oxide-cGMP-mediated signaling / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / endosome lumen / 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 / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / Golgi lumen / positive regulation of protein localization to nucleus / cognition / glucose metabolic process / vasodilation / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / 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
PHENOL / MYRISTIC ACID / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsAyan, E. / Bahar, I.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government Turkey
CitationJournal: To Be Published
Title: hexamer form of insulin detemir at ambient temperature
Authors: Ayan, E. / Bahar, I.
History
DepositionFeb 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: 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
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,28012
Polymers11,4334
Non-polymers8478
Water905
1
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,83936
Polymers34,29912
Non-polymers2,54024
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area26320 Å2
ΔGint-938 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.240, 81.240, 40.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-102-

ZN

21D-102-

ZN

31D-103-

CL

41B-203-

HOH

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide Insulin A chain / Small 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: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3332.849 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308

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Non-polymers , 5 types, 13 molecules

#3: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium acetate trihydrate, 0.1M tris hydrochloride pH 9

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5 Å
DetectorType: RIGAKU HyPix-Arc 100 / Detector: PIXEL / Date: Aug 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.85→19.38 Å / Num. obs: 2306 / % possible obs: 98.53 % / Redundancy: 19 % / CC1/2: 0.89 / Net I/σ(I): 7.39
Reflection shellResolution: 2.85→2.951 Å / Num. unique obs: 202 / CC1/2: 0.745

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→19.38 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3377 234 10.26 %
Rwork0.2852 --
obs0.2905 2281 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→19.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 48 5 849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.349
X-RAY DIFFRACTIONf_dihedral_angle_d14.414315
X-RAY DIFFRACTIONf_chiral_restr0.032122
X-RAY DIFFRACTIONf_plane_restr0.002145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.950.4438220.3955182X-RAY DIFFRACTION94
2.95-3.070.3696220.3509211X-RAY DIFFRACTION98
3.07-3.210.3753240.3505203X-RAY DIFFRACTION99
3.21-3.370.4327260.3215217X-RAY DIFFRACTION100
3.38-3.580.3989230.3284195X-RAY DIFFRACTION100
3.59-3.860.4106220.2998208X-RAY DIFFRACTION100
3.86-4.240.3555240.2757198X-RAY DIFFRACTION100
4.25-4.850.2984250.227221X-RAY DIFFRACTION100
4.87-6.050.2849230.2846206X-RAY DIFFRACTION100
6.1-100.2793230.2435206X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0822-0.2701-0.13330.90750.49480.3764-0.10320.0242-0.20530.02040.0042-0.22680.14830.2793-0.01790.32250.31860.07251.2025-0.18111.0956-8.590513.6758-5.9745
23.1012-0.2721-0.98731.860.04180.3150.1152-0.40010.32510.42480.2627-0.2021-0.17740.5212-0.07241.0645-0.13330.58110.7727-0.47231.1577-11.48756.6442-5.9909
33.1636-2.18981.9063.72760.67632.94550.01730.0473-0.7785-0.2531-0.65181.39340.4626-0.87980.43350.59320.0175-0.05330.4508-0.22740.8135-15.214813.0008-15.1358
42.86230.2422-2.27473.3132-0.0241.8194-0.0894-0.2074-0.16730.15290.20530.1227-0.21050.68350.35020.1254-0.0430.09710.66960.11710.206-3.61597.483-13.1451
52.95550.3330.05084.1476-0.36950.286-0.5454-0.46510.0555-0.14180.7510.1765-0.115-0.0640.23620.53270.33550.15460.7690.26280.1941-7.434516.5718-17.7378
64.0475-3.24762.11722.9603-1.87471.19370.4945-0.67030.50450.62650.3678-0.1933-0.34580.0262-0.54751.0659-0.23070.29710.7394-0.06220.44181.582915.8133-32.7055
72.6191-1.79951.5251.4381-0.59791.8831-0.0872-0.1314-0.14480.33910.3302-0.3490.25110.0673-0.33160.72240.21030.29250.27590.09360.98587.262911.7603-32.4759
80.9679-2.01650.24095.7357-0.42335.50250.20120.56120.59270.2036-0.2769-0.34080.71771.30980.01530.55440.0497-0.13971.1166-0.46680.57477.684519.078-23.2965
91.8601-1.2908-0.75462.06690.58221.2198-0.13580.2896-0.1298-0.1625-0.44550.5541-0.4128-0.3383-0.93160.66590.58910.18170.2838-0.15910.2549-0.18038.1077-25.26
102.9557-0.24641.42523.40621.87792.9226-0.0851-0.32220.36740.0130.1748-0.0514-0.39940.04260.17441.19690.50590.1140.5088-0.30150.9067-1.549817.6239-21.0576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 12 )
3X-RAY DIFFRACTION3chain 'A' and (resid 13 through 21 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 19 )
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 29 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 6 )
7X-RAY DIFFRACTION7chain 'C' and (resid 7 through 12 )
8X-RAY DIFFRACTION8chain 'C' and (resid 13 through 21 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 19 )
10X-RAY DIFFRACTION10chain 'D' and (resid 20 through 29 )

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