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- PDB-8ipz: Crystal structure of insulin detemir -

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Basic information

Entry
Database: PDB / ID: 8ipz
TitleCrystal structure of insulin detemir
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin / detemir / Turkish light source
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 / activation of protein kinase B activity / negative regulation of respiratory burst involved in inflammatory response / 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 / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / 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 protein secretion / positive regulation of D-glucose import across plasma membrane / 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 / cognition / vasodilation / 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: 1.4 Å
AuthorsDeMirci, H. / Ayan, E.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Crystal structure of insulin detemir
Authors: DeMirci, H. / Ayan, E.
History
DepositionMar 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
Water3,909217
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 area22880 Å2
ΔGint-805 kcal/mol
Surface area11160 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_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area25330 Å2
ΔGint-799 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.874, 78.874, 79.282
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

61F-103-

CL

71H-102-

ZN

81H-103-

CL

91B-230-

HOH

101F-223-

HOH

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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, 233 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.: 217 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium acetate trihydrate, 0.1M TRIS hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Feb 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.4→22.77 Å / Num. obs: 36231 / % possible obs: 99.8 % / Redundancy: 1 % / CC1/2: 0.99 / Net I/σ(I): 13.91
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 2608 / CC1/2: 0.21

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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: 1.4→22.77 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2003 6.17 %
Rwork0.1921 --
obs0.1945 32445 89.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→22.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 96 217 1905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111728
X-RAY DIFFRACTIONf_angle_d1.482306
X-RAY DIFFRACTIONf_dihedral_angle_d17.449630
X-RAY DIFFRACTIONf_chiral_restr0.109244
X-RAY DIFFRACTIONf_plane_restr0.01290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.40131160.36811733X-RAY DIFFRACTION71
1.44-1.470.34971230.33231833X-RAY DIFFRACTION76
1.47-1.520.37551330.29771891X-RAY DIFFRACTION78
1.52-1.570.32261270.25831967X-RAY DIFFRACTION82
1.57-1.620.27521380.23032083X-RAY DIFFRACTION84
1.62-1.690.28661430.21732121X-RAY DIFFRACTION88
1.69-1.760.2491390.20442197X-RAY DIFFRACTION91
1.76-1.860.24831510.19112263X-RAY DIFFRACTION93
1.86-1.970.21811460.18032318X-RAY DIFFRACTION95
1.97-2.130.21591590.1732400X-RAY DIFFRACTION98
2.13-2.340.22461550.18272364X-RAY DIFFRACTION99
2.34-2.680.21131590.18662425X-RAY DIFFRACTION99
2.68-3.370.221540.18592420X-RAY DIFFRACTION100
3.37-100.19291600.16082427X-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)
12.14690.47311.1778.2339-2.79299.520.0057-0.1674-0.11410.4599-0.01690.3575-0.0442-0.451-0.15290.1567-0.02170.00270.2584-0.02570.1604-15.41680.231512.8916
22.62650.99543.875.99253.0116.29020.1545-0.2619-0.16870.4049-0.0809-0.14840.2685-0.2148-0.0680.1502-0.0336-0.01380.22080.01020.1601-11.7449-5.689413.1315
34.40590.07370.06299.031-1.95973.71830.2151-0.46960.3788-0.21440.06210.64280.2219-0.5763-0.28920.1025-0.0632-0.01460.20890.01930.1726-18.7871-5.80483.9747
43.23691.82261.15383.71831.30052.36680.04-0.00950.0432-0.0361-0.05490.08440.0047-0.1220.00640.1313-0.00170.01170.11520.01890.1037-9.80330.37864.0528
51.8553-0.4113-0.26686.56463.84233.0199-0.1518-1.07220.40250.0489-0.04260.8986-0.1043-0.75480.26220.16180.02710.01780.3627-0.03050.2613-17.01626.02574.4034
62.80891.1999-0.19834.33341.83735.28020.16130.27850.3173-0.7817-0.24550.1467-0.34370.03370.04940.23610.07070.00650.2210.04890.1615-8.698311.0638-13.2954
74.6161.0495-4.10964.3055-2.25695.35520.3178-0.35840.53390.5679-0.33810.2166-0.74510.5819-0.18180.17260.02410.01030.1785-0.00140.1884-11.39516.2792-4.1011
82.9004-1.0518-1.29035.66122.53773.65150.0156-0.0074-0.03320.0171-0.06120.04710.0356-0.09240.08850.0947-0.0002-0.00580.07790.02320.063-7.69715.6801-4.1361
92.59152.52221.08724.43873.6193.98320.10430.57680.06-0.3553-0.48841.1038-0.0175-0.84010.58610.28650.0363-0.07120.3193-0.01210.2164-15.89625.6759-5.8549
104.1981-0.136-1.42441.42290.8644.6999-0.163-0.4883-0.35840.2950.059-0.10370.34130.00620.11940.26030.1173-0.01770.30660.01750.1777-28.568414.0455-0.5186
114.40182.38711.53554.96142.40433.7635-0.17310.1165-0.20920.19170.0591-0.17730.31320.40820.04660.21140.0973-0.01870.21620.02640.2182-23.259311.2403-9.2653
126.0755-0.8607-2.01593.81471.0193.9689-0.1539-0.1823-0.12320.19410.0868-0.01450.27870.05120.04730.0904-0.01-0.02540.07460.02080.072-33.821614.5711-9.2747
132.37011.4470.44751.5349-0.86692.0429-0.3949-1.001-0.99811.33490.4798-0.40341.26960.30230.02060.60180.12610.04080.32140.14210.1627-34.43485.565-8.6485
146.7494-1.1244-2.19581.7846-0.63654.0989-0.24090.3435-0.2835-0.26730.0810.20030.1375-0.01410.19390.1912-0.0153-0.00950.13280.00640.1343-42.89749.1013-26.6424
156.0441-3.59371.14537.3758-2.27167.5052-0.2632-0.0765-0.83460.0337-0.00370.21650.24-1.0295-0.17950.1483-0.03290.03210.10690.03050.1759-45.974.0976-17.5919
163.94631.3851-2.00753.0736-1.82355.8988-0.0986-0.0058-0.02770.0340.0656-0.01490.102-0.07460.050.08560.0056-0.00490.0532-0.00670.0893-39.506613.2571-17.4915
176.79440.4835-1.72862.6464-1.12642.2197-0.20860.4979-0.6378-0.694-0.0705-0.40460.51570.1440.6460.30730.01460.03070.1553-0.04940.1773-34.71866.3062-18.9435
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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