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

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Basic information

Entry
Database: PDB / ID: 9lvd
TitleTemperature induces a shift from the dihexamer to the hexamer form of insulin (200K)
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin dihexamer / insulin hexamer / temperature jump scXRD
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: 2.85 Å
AuthorsAyan, E. / Kepceoglu, A.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government Turkey
CitationJournal: To Be Published
Title: Temperature induces a shift from the dihexamer to the hexamer form of insulin (200K)
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,28012
Polymers11,4334
Non-polymers8478
Water181
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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area26580 Å2
ΔGint-934 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.711, 80.711, 39.640
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

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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, 9 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.: 1 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
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: 200 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: 2.85→17.56 Å / Num. obs: 2306 / % possible obs: 98.53 % / Redundancy: 20 % / CC1/2: 0.934 / Net I/σ(I): 6.46
Reflection shellResolution: 2.85→2.951 Å / Num. unique obs: 202 / CC1/2: 0.33

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→17.55 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 34.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.33 220 9.72 %
Rwork0.28 --
obs0.3 2264 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→17.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 48 1 845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002864
X-RAY DIFFRACTIONf_angle_d0.4321153
X-RAY DIFFRACTIONf_dihedral_angle_d16.547315
X-RAY DIFFRACTIONf_chiral_restr0.033122
X-RAY DIFFRACTIONf_plane_restr0.002145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9510.3702170.362189X-RAY DIFFRACTION93
2.93-3.050.3739220.3665209X-RAY DIFFRACTION99
3.05-3.190.413220.3901205X-RAY DIFFRACTION99
3.19-3.350.4167220.3693219X-RAY DIFFRACTION100
3.36-3.560.414230.3336186X-RAY DIFFRACTION99
3.56-3.830.4338230.3408210X-RAY DIFFRACTION99
3.84-4.220.3405230.2875198X-RAY DIFFRACTION100
4.22-4.820.3964240.2786220X-RAY DIFFRACTION100
4.84-5.990.4105200.3254203X-RAY DIFFRACTION100
6.05-100.2876240.2703205X-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)
11.52750.81830.90931.6150.6460.9459-0.2067-0.4359-0.00910.63230.1919-0.19870.00790.04040.07680.73510.4215-0.30580.5938-0.06590.6302-8.540113.578833.9559
20.57470.948-0.64652.72051.06274.66450.2524-0.5890.01260.4514-0.080.01450.13940.29220.26861.18990.04320.72350.7410.04980.8374-11.37956.50833.892
30.01450.079-0.0090.3965-0.03730.00240.1961-0.18520.08210.2225-0.23230.2-0.3412-0.18450.02050.804-0.16920.29030.8851-0.25020.2994-15.038812.947824.9889
43.20280.1254-1.88864.73160.42022.21930.0464-0.0380.2121-0.11170.2364-0.25320.01310.32370.41810.3848-0.144-0.30290.41560.1234-0.0779-5.25578.640224.7517
50.48050.0165-0.49184.34354.45695.1072-0.4367-0.57530.8436-0.01220.01130.2909-0.8332-1.07360.40190.50550.29240.09531.0311-0.23610.7649-4.490717.360326.1833
60.95961.468-0.51622.45450.22275.24810.02170.08340.4274-0.02730.1716-0.4588-0.5698-0.53150.00450.4697-0.057-0.0820.31410.10370.42754.287613.68787.7564
70.63690.29980.93783.2641.40784.57790.31020.61270.3486-0.0531-0.1602-0.25750.36771.189-0.04231.03810.1134-0.08750.7744-0.21350.38837.791118.93316.804
80.9392-0.1728-0.55250.95040.21760.53950.10760.16540.1105-0.2619-0.27370.401-0.2217-0.3284-0.72650.5910.79280.03110.5195-0.47680.04610.59639.621916.5662
93.9863-2.64252.29324.8216-2.87973.07480.0435-0.11280.32670.149-0.03380.1203-0.4755-0.18460.51620.46910.1771-0.13230.2224-0.28460.4529-4.205217.088315.3974
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 )

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