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- PDB-8hgz: Crystal structure of insulin -

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Basic information

Entry
Database: PDB / ID: 8hgz
TitleCrystal structure of insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin / long-acting analog / insulin receptor / insulin dynamics
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 fatty acid metabolic process / negative regulation of feeding behavior / 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 fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / 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 / regulation of cellular amino acid metabolic process / 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 / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / 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 glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / 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 / protease binding / secretory granule lumen / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / 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
PHENOL / MYRISTIC ACID / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDeMirci, H. / Ayan, E.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government Turkey
CitationJournal: Crystals / Year: 2023
Title: Comparative Study of High-Resolution LysB29(N epsilon-myristoyl) des(B30) Insulin Structures Display Novel Dynamic Causal Interrelations in Monomeric-Dimeric Motions
Authors: Ayan, E. / Destan, E. / Kepceoglu, A. / Ciftci, H.I. / Kati, A. / DeMirci, H.
History
DepositionNov 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Insulin A chain
F: Insulin B chain
A: Insulin A chain
B: Insulin B chain
I: Insulin A chain
J: Insulin B chain
M: Insulin A chain
N: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,65425
Polymers22,8668
Non-polymers1,78717
Water3,387188
1
E: Insulin A chain
F: Insulin B chain
hetero molecules

I: Insulin A chain
J: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,37413
Polymers11,4334
Non-polymers9419
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4590 Å2
ΔGint-25 kcal/mol
Surface area6830 Å2
MethodPISA
2
A: Insulin A chain
B: Insulin B chain
M: Insulin A chain
N: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,28012
Polymers11,4334
Non-polymers8478
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-31 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.885, 78.885, 79.272
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
11F-102-

ZN

21F-103-

CL

31B-101-

ZN

41B-102-

CL

51J-102-

ZN

61J-103-

CL

71N-101-

ZN

81N-102-

CL

91J-229-

HOH

101N-216-

HOH

111N-219-

HOH

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Components

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Protein/peptide , 2 types, 8 molecules EAIMFBJN

#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, 205 molecules

#3: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 5 / 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.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 40.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium acetate trihydrate, 0.1M tris hydrochloride pH 9

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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 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.7→21.64 Å / Num. obs: 110176 / % possible obs: 96.94 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.33
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 9012 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XDA

1xda


Resolution: 1.7→21.64 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 1939 9.88 %
Rwork0.2175 --
obs0.2214 19616 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→21.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 103 188 1883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021727
X-RAY DIFFRACTIONf_angle_d0.3662304
X-RAY DIFFRACTIONf_dihedral_angle_d12.877624
X-RAY DIFFRACTIONf_chiral_restr0.031244
X-RAY DIFFRACTIONf_plane_restr0.002289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.31561250.27131198X-RAY DIFFRACTION91
1.74-1.790.32911310.26831163X-RAY DIFFRACTION91
1.79-1.840.30541320.24931229X-RAY DIFFRACTION94
1.84-1.90.29791350.24421215X-RAY DIFFRACTION94
1.9-1.970.25511430.24111260X-RAY DIFFRACTION96
1.97-2.050.25661420.23511265X-RAY DIFFRACTION98
2.05-2.140.291400.23441275X-RAY DIFFRACTION98
2.14-2.250.24711410.221306X-RAY DIFFRACTION99
2.25-2.40.22871450.21293X-RAY DIFFRACTION99
2.4-2.580.27541340.23151270X-RAY DIFFRACTION99
2.58-2.840.22821410.21285X-RAY DIFFRACTION100
2.84-3.250.29461470.21971301X-RAY DIFFRACTION100
3.25-4.090.23691440.18951314X-RAY DIFFRACTION100
4.09-210.23221390.18021303X-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)
13.7895-2.15960.58344.0859-4.34985.68410.10740.5910.1143-0.3490.25720.37870.627-0.3342-0.28320.25840.0274-0.0320.26420.02360.2223-12.00429.75770.3263
22.25172.38842.27552.50632.37792.3821-0.10690.2930.265-0.45350.4601-0.0864-0.3640.6675-0.41910.27730.03640.08190.2630.03920.2196-5.357812.30780.0729
36.24683.4778-4.22226.7241-3.02393.51550.7338-0.33960.44350.2402-0.54350.0381-1.2896-0.0523-0.14640.22320.04310.01820.17160.0180.2405-11.752216.40549.2134
43.6481-1.6503-0.75036.24823.21526.76080.05650.1078-0.08580.0877-0.03240.12710.1933-0.2710.02570.1387-0.03310.02850.1030.02280.0851-7.77555.59959.1705
56.4122.1555-1.71767.5156-5.0893.49520.30091.20550.1122-0.8771-0.12890.62550.1605-0.3004-0.13840.24970.0977-0.03870.33970.00690.1661-16.11755.74987.3937
62.7140.9875-2.59583.4466-1.89982.7503-0.10020.2823-0.1697-0.33430.06750.09830.09650.01730.10670.1979-0.0162-0.02440.14670.00650.1306-3.379531.922113.3331
78.4546-4.99494.13956.5271-2.97873.4438-0.0721-0.5205-0.62330.04770.1020.02720.2048-0.6665-0.05460.1999-0.03830.00090.11790.03640.1697-6.312326.552621.9711
86.07152.7377-3.51824.437-2.55447.4681-0.1296-0.0091-0.0505-0.07220.13030.08540.2702-0.1052-0.02570.07220.006-0.01630.0489-0.01820.08720.013136.016922.3119
97.27242.77473.80228.5994-2.35983.92160.27840.648-0.3056-0.273-0.1873-0.8329-0.47650.2648-0.03820.29580.08560.04760.15360.02590.25344.657429.00220.6069
109.23795.0236-4.15058.99061.15133.74410.0246-0.70030.01160.1249-0.071-0.19780.07760.31220.080.19620.0234-0.00950.17750.00190.09577.913713.227526.1395
113.8926-5.2184.30689.1004-8.95149.9495-0.1129-0.1221-0.13390.44890.29940.5368-0.7599-0.0097-0.22040.2179-0.02210.02410.10490.00370.16190.943813.000126.4811
127.0341-2.0688-3.03584.55061.19944.29170.11480.210.3236-0.03870.1557-0.405-0.30410.0198-0.31090.2638-0.04140.01910.1008-0.01230.20354.346819.234317.2966
132.6505-1.87770.84766.9878-3.09094.2655-0.00340.0598-0.0476-0.01250.0053-0.06860.07540.14370.03870.08660.0023-0.00170.0884-0.02550.07555.15757.958217.4228
147.28610.8042-0.08415.95356.527.26110.1234-0.08110.32110.7727-0.3074-0.68520.56190.43960.19510.218-0.0543-0.01350.14360.0440.202813.524511.602218.3138
155.92442.08692.50994.22185.13556.2764-0.3389-1.7627-0.95960.3034-0.488-0.60830.5725-0.06010.6270.2620.10820.06810.42470.10920.27289.476433.412339.1919
167.51832.2662-3.36144.1686-0.61761.55-0.0134-0.3921-0.44210.62370.2005-0.22380.42130.6615-0.12880.16280.1065-0.03460.3647-0.02370.139312.065740.040839.374
174.16213.25261.73733.99672.35093.2964-0.0807-0.051-0.1153-0.0955-0.15360.05390.31730.21310.12770.20920.10460.01130.23330.07460.207416.157233.907730.482
186.5959-1.0454-3.85654.73371.25693.4601-0.0055-0.1062-0.16120.1254-0.0179-0.08750.3054-0.05740.06210.1063-0.0038-0.04010.16820.00620.0975.350637.573630.5729
193.63062.50332.55763.81441.09351.963-0.3849-1.4849-0.5861.62110.68350.01390.88680.11760.160.51440.14470.02090.33290.12090.18724.937428.658531.6251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'E' and (resid 7 through 12 )
3X-RAY DIFFRACTION3chain 'E' and (resid 13 through 21 )
4X-RAY DIFFRACTION4chain 'F' and (resid 1 through 22 )
5X-RAY DIFFRACTION5chain 'F' and (resid 23 through 29 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1 through 12 )
7X-RAY DIFFRACTION7chain 'A' and (resid 13 through 21 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 29 )
10X-RAY DIFFRACTION10chain 'I' and (resid 1 through 6 )
11X-RAY DIFFRACTION11chain 'I' and (resid 7 through 12 )
12X-RAY DIFFRACTION12chain 'I' and (resid 13 through 21 )
13X-RAY DIFFRACTION13chain 'J' and (resid 1 through 22 )
14X-RAY DIFFRACTION14chain 'J' and (resid 23 through 29 )
15X-RAY DIFFRACTION15chain 'M' and (resid 1 through 6 )
16X-RAY DIFFRACTION16chain 'M' and (resid 7 through 12 )
17X-RAY DIFFRACTION17chain 'M' and (resid 13 through 21 )
18X-RAY DIFFRACTION18chain 'N' and (resid 1 through 22 )
19X-RAY DIFFRACTION19chain 'N' and (resid 23 through 29 )

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