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

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Basic information

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


negative regulation of glycogen catabolic 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 / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...negative regulation of glycogen catabolic 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 / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / 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 / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / 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 / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / 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 / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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: 2.7 Å
AuthorsAyan, E. / Bahar, I.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government Turkey
CitationJournal: To Be Published
Title: di-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
E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,56024
Polymers22,8668
Non-polymers1,69316
Water2,756153
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
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area24440 Å2
ΔGint-932 kcal/mol
Surface area10180 Å2
MethodPISA
2
E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
hetero molecules

E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
hetero molecules

E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,83936
Polymers34,29912
Non-polymers2,54024
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area26730 Å2
ΔGint-839 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.898, 80.898, 80.414
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

21B-103-

CL

31D-102-

ZN

41D-103-

CL

51F-102-

ZN

61H-102-

ZN

71H-103-

CL

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Components

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Protein/peptide , 2 types, 8 molecules ACEGBDFH

#1: Protein/peptide
Insulin A chain / Small chain


Mass: 2383.698 Da / Num. of mol.: 4
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.: 4
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, 169 molecules

#3: Chemical
ChemComp-IPH / PHENOL


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
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 150 / 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: 2.7→19.32 Å / Num. obs: 5361 / % possible obs: 97.3 % / Redundancy: 12.9 % / CC1/2: 0.884 / Net I/σ(I): 5.81
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 479 / CC1/2: 0.737

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.32 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 36.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3223 527 10.07 %
Rwork0.2728 --
obs0.2778 5233 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 96 153 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021723
X-RAY DIFFRACTIONf_angle_d0.3962299
X-RAY DIFFRACTIONf_dihedral_angle_d16.053627
X-RAY DIFFRACTIONf_chiral_restr0.032242
X-RAY DIFFRACTIONf_plane_restr0.002290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80.3506500.3372431X-RAY DIFFRACTION93
2.8-2.910.3445520.327460X-RAY DIFFRACTION96
2.91-3.040.3503530.3042476X-RAY DIFFRACTION97
3.04-3.20.339560.2966464X-RAY DIFFRACTION97
3.2-3.40.304540.2858486X-RAY DIFFRACTION99
3.4-3.660.3635490.2853471X-RAY DIFFRACTION98
3.66-4.020.4263530.2693476X-RAY DIFFRACTION98
4.03-4.60.2732520.2318485X-RAY DIFFRACTION100
4.6-5.750.2719570.236479X-RAY DIFFRACTION99
5.77-100.285510.2663478X-RAY DIFFRACTION97
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)
14.1768-2.3062-0.56481.40840.71921.30450.17780.25170.281-0.1946-0.1619-0.1581-0.11170.0181-0.21250.3640.27730.29110.29950.21530.6506-12.69399.4242-37.0718
20.33240.51130.2811.8356-0.58512.186-0.01090.24880.0269-0.7429-0.1811-0.12030.4397-0.1363-0.04680.4280.16380.09960.50120.07530.4585-6.136412.2734-37.1769
33.44811.0910.30892.3305-1.82292.99720.2515-0.16340.5595-0.22430.520.3847-0.4106-0.3763-0.18790.37490.01280.16680.20350.02180.5687-12.468916.3244-28.3139
43.4907-0.5258-0.28853.9467-0.77072.0558-0.14480.28620.37830.1404-0.1430.16120.0461-0.4304-0.16070.25950.00040.10260.19220.10960.3466-8.24775.8202-28.1985
53.01920.3421-0.72931.5641-0.85082.66770.05950.41930.077-0.31080.15440.09090.0609-0.30960.57210.3829-0.11780.11020.45730.08350.0977-16.90455.4763-29.3504
62.59261.14362.0232.2685-1.43364.6501-0.0032-0.40920.32110.23070.0950.4243-0.0241-0.6835-0.23050.2096-0.0445-0.05030.33250.01580.3896-13.8475-3.3317-10.7462
70.2498-0.48241.14211.7343-2.94725.87660.02830.13660.0914-0.3775-0.11550.10990.86460.2574-0.15280.3713-0.12680.10760.44870.02150.1925-19.1858-6.3531-19.9522
84.4056-0.4645-1.22733.17-0.49172.05070.3501-0.49610.30860.12910.19440.1468-0.08560.25080.57070.5628-0.0560.02550.17060.04080.1539-9.65840.1903-19.9252
94.1622-1.56041.00526.68460.76363.5603-0.0245-0.35680.0176-0.00330.12060.1695-0.2721-0.39840.19720.36870.3789-0.03920.51580.23390.1972-16.84455.5496-18.8158
100.52540.3765-0.22910.8588-0.21850.29040.05850.00860.09540.1018-0.05590.2165-0.0966-0.1699-0.03430.06450.02120.18320.228-0.0070.5698-10.083710.14932.8991
113.37392.0252-0.20471.225-0.15651.4780.047-0.07060.21250.12360.56940.4635-0.2419-0.0205-0.03540.33520.11270.13640.2756-0.03090.5244-13.33315.395911.9296
122.78451.02460.65931.8326-0.55175.0507-0.34970.3030.15030.1591-0.13650.3091-0.5677-0.4133-0.92160.06560.03740.2840.2807-0.077-0.0672-8.5665.164211.9251
132.1515-0.22640.45770.0975-0.22970.55160.21580.4313-0.187-0.1401-0.06790.07780.0455-0.00850.61790.32330.3470.1470.3273-0.167-0.0276-17.26474.549410.7921
143.7010.3350.35813.3317-0.63892.41550.1806-0.2540.61580.78230.5090.389-0.2212-0.3094-0.13090.38360.03260.08170.44750.12430.1701-13.5271-4.446129.2733
150.34210.9714-0.05973.4758-1.31881.7930.00450.07290.1271-0.2863-0.25490.3668-0.1308-0.5369-0.40860.34090.0266-0.00830.18860.01270.3938-18.657-7.722420.1662
163.72560.68050.99744.42280.69043.4610.2454-0.13820.30940.38210.09790.0188-0.13490.1423-0.10130.19730.0573-0.00210.24440.09390.1348-9.6612-0.307420.3021
178.68-0.37090.86758.5528-0.42432.87030.0367-0.65670.24680.92520.17670.376-0.4123-0.4358-0.11140.23460.05830.18920.39260.23190.3953-17.05384.505621.4188
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 22 )
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 29 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 12 )
7X-RAY DIFFRACTION7chain 'C' and (resid 13 through 21 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 22 )
9X-RAY DIFFRACTION9chain 'D' and (resid 23 through 29 )
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 12 )
11X-RAY DIFFRACTION11chain 'E' and (resid 13 through 21 )
12X-RAY DIFFRACTION12chain 'F' and (resid 1 through 22 )
13X-RAY DIFFRACTION13chain 'F' and (resid 23 through 29 )
14X-RAY DIFFRACTION14chain 'G' and (resid 1 through 12 )
15X-RAY DIFFRACTION15chain 'G' and (resid 13 through 21 )
16X-RAY DIFFRACTION16chain 'H' and (resid 1 through 22 )
17X-RAY DIFFRACTION17chain 'H' and (resid 23 through 29 )

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