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- PDB-9lvc: Temperature induces a shift from the dihexamer to the hexamer for... -

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Basic information

Entry
Database: PDB / ID: 9lvc
TitleTemperature induces a shift from the dihexamer to the hexamer form of insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin structure / hexamer form / temperature jump
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 / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / regulation of protein secretion / Insulin processing / 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 / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / 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 / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / COPI-mediated anterograde transport / transport vesicle / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / 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 nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / acute-phase response / endosome lumen / positive regulation of protein secretion / positive regulation of D-glucose import / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / 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 / protease binding / positive regulation of cell growth / 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 / 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-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: 2.3 Å
AuthorsAyan, E. / Kepceoglu, A.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Temperature induces a shift from the dihexamer to the hexamer form of insulin
Authors: Ayan, E. / Kepceoglu, A.
History
DepositionFeb 12, 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
Water97354
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_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area21110 Å2
ΔGint-560 kcal/mol
Surface area14140 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_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area18550 Å2
ΔGint-578 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.064, 79.064, 79.496
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-208-

HOH

101F-208-

HOH

111F-210-

HOH

121H-204-

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, 70 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.: 54 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 293 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: 100 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: Sep 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.3→19.77 Å / Num. obs: 8131 / % possible obs: 98.77 % / Redundancy: 4.1 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 30.01
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 8131 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.77 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 30.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2868 809 9.95 %
Rwork0.2321 --
obs0.2375 8131 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 96 54 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.381
X-RAY DIFFRACTIONf_dihedral_angle_d14.517630
X-RAY DIFFRACTIONf_chiral_restr0.033244
X-RAY DIFFRACTIONf_plane_restr0.002290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.2653820.2573731X-RAY DIFFRACTION99
2.38-2.480.349840.2601715X-RAY DIFFRACTION98
2.48-2.590.3193770.2505729X-RAY DIFFRACTION99
2.59-2.730.2653820.2573737X-RAY DIFFRACTION99
2.73-2.90.3198800.2624729X-RAY DIFFRACTION99
2.9-3.120.2874830.2464745X-RAY DIFFRACTION99
3.12-3.430.2837810.2331724X-RAY DIFFRACTION100
3.43-3.920.2766830.2224741X-RAY DIFFRACTION100
3.93-4.930.2713770.1917734X-RAY DIFFRACTION98
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)
16.2406-2.2584-1.44291.9999-4.78686.2196-0.0454-1.0401-0.08491.0972-0.0224-0.5457-0.31240.45210.28210.15940.02770.00810.31950.1580.333413.79938.077434.2361
27.85960.14841.97916.41825.62825.93650.6006-0.10420.0492-0.1773-0.3146-0.2256-0.03950.24560.06760.08110.0120.00660.1476-0.05390.164613.150445.413834.2208
32.0384-0.62010.85764.0565-0.03643.4379-0.04780.5830.3545-0.27120.1833-0.6096-0.47680.627-0.18220.1127-0.04790.05290.2785-0.06230.219219.51341.60225.3811
43.7371.4467-1.6932.6004-0.52221.782-0.0683-0.07810.3010.23830.0917-0.2446-0.0353-0.1055-0.13170.08110.0505-0.01880.149-0.02620.16516.482540.992327.131
55.4426-0.5612-0.45081.26351.37391.4977-0.1685-0.7328-0.352-0.31530.0356-0.51270.45140.53070.22630.04140.15340.23710.28070.0140.071414.533235.231422.6005
61.9226-1.5196-0.30951.44130.98672.3399-0.18070.2953-0.4784-0.5546-0.1774-0.0108-0.19070.26750.24460.4746-0.09410.11770.2878-0.04240.28685.580631.28547.7139
71.0630.27250.36360.2235-0.45342.08770.2110.008-0.0553-0.2653-0.1033-0.02790.3688-0.42220.97310.4808-0.0253-0.00870.1507-0.02080.1243-1.304132.44388.0512
88.04652.46222.45243.54720.68222.79480.41220.2706-0.44570.22770.1041-0.4290.19440.1175-0.04880.2578-0.02160.04620.1462-0.0190.17482.020925.836916.931
92.55470.33660.43814.7959-2.71784.68060.12430.21530.1469-0.0278-0.3265-0.12220.03860.82770.04230.082-0.06260.02320.17170.00980.18964.167938.68315.1279
104.6691.13050.38628.0226-1.62263.8192-0.070.7069-0.5426-1.01690.3855-0.41750.39490.0004-0.19860.27370.1338-0.07070.4556-0.03920.168110.072231.223219.2427
116.3364-0.9781.78952.9752-0.5458.49740.1587-0.9642-0.35770.4204-0.1327-0.4492-0.02180.3137-0.48690.32240.058-0.02080.2895-0.00460.325914.392839.7426-5.6538
120.4707-0.3638-0.5510.28050.42310.6460.2309-0.12710.3543-0.44560.595-0.6712-0.56691.18652.18560.2161-0.06120.06980.4532-0.43280.252113.315147.0997-5.6761
131.61221.38440.99314.05421.27574.1045-0.31250.27380.2347-0.6902-0.06230.1894-0.55230.4162-0.15710.1537-0.0140.03330.2842-0.01030.283319.970843.5926-14.5228
145.05590.5132-2.04932.2438-0.13033.0084-0.449-0.2299-0.19650.1420.23270.13930.57030.0664-0.160.23290.03750.01430.1422-0.0060.19826.93541.7168-12.7849
155.05820.11340.31672.37021.8971.8331-0.1141-0.3549-0.07320.220.2734-0.04930.65740.30180.15920.16280.04790.03070.3763-0.07390.082415.406436.6184-17.1525
161.8522-0.85650.75783.4546-0.05151.1739-0.2002-0.1230.0388-0.4792-0.04950.2982-0.13960.09340.00440.146-0.05620.0220.25290.02060.17047.833732.1093-32.0719
173.84041.00710.21843.05730.69811.1943-0.1544-0.25760.03460.47120.4782-0.11420.46120.16550.33760.2250.0436-0.05370.07250.02180.15920.855232.5338-32.0693
185.0316-0.31180.20740.47260.65254.0614-0.15190.293-0.2168-0.0056-0.1724-0.3899-0.2861-0.3381-0.27530.17220.02360.02690.1339-0.00970.30354.252226.36-22.8353
190.9752-0.22390.68592.3631-1.92842.0094-0.06070.0040.2111-0.0763-0.2396-0.2788-0.10110.1829-0.01010.1469-0.0228-0.00930.1315-0.0210.16844.921339.3024-24.7247
206.15920.8182-0.4956.7925-1.96236.5711-0.16180.3431-0.1126-0.5033-0.5366-0.27160.1238-0.3124-0.04620.21580.01-0.08240.2555-0.02560.272611.452532.2288-20.3563
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 )
11X-RAY DIFFRACTION11chain 'E' and (resid 1 through 6 )
12X-RAY DIFFRACTION12chain 'E' and (resid 7 through 12 )
13X-RAY DIFFRACTION13chain 'E' and (resid 13 through 21 )
14X-RAY DIFFRACTION14chain 'F' and (resid 1 through 19 )
15X-RAY DIFFRACTION15chain 'F' and (resid 20 through 29 )
16X-RAY DIFFRACTION16chain 'G' and (resid 1 through 6 )
17X-RAY DIFFRACTION17chain 'G' and (resid 7 through 12 )
18X-RAY DIFFRACTION18chain 'G' and (resid 13 through 21 )
19X-RAY DIFFRACTION19chain 'H' and (resid 1 through 19 )
20X-RAY DIFFRACTION20chain 'H' and (resid 20 through 29 )

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