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- PDB-9utk: Monoclinic crystal structure of acid-stable protracted insulin (293 K) -

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Basic information

Entry
Database: PDB / ID: 9utk
TitleMonoclinic crystal structure of acid-stable protracted insulin (293 K)
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / Diabetes / Insulin / Structural biology / Molecular dynamics
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 protein secretion / positive regulation of D-glucose import / 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 / glucose homeostasis / cell-cell signaling / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsAyan, E. / Demirci, H.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Small Struct / Year: 2025
Title: Triple Calcium Binding Stoichiometry in the Monoclinic Crystal Form of Protracted Insulin
Authors: Ayan, E. / Engilberge, S. / Yokoi, S. / Orlans, J. / de Sanctis, D. / Basu, S. / Rive-Mathieu, E. / Kepceoglu, A. / Mitsutake, A. / Demirci, H.
History
DepositionMay 4, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 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
I: Insulin A chain
J: Insulin B chain
K: Insulin A chain
L: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,45025
Polymers34,56412
Non-polymers88713
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18670 Å2
ΔGint-272 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.730, 62.220, 56.390
Angle α, β, γ (deg.)90.00, 111.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
Insulin A chain


Mass: 2326.647 Da / Num. of mol.: 6
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: 3433.953 Da / Num. of mol.: 6
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, 53 molecules

#3: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 200mM CaCl2 buffered in 100mM Tris-HCl pH 8,5, 30% (v/v) 2-Methyl-2,4-pentanediol, 8% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Mar 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→19.56 Å / Num. obs: 16759 / % possible obs: 93.4 % / Redundancy: 2 % / CC1/2: 0.825 / Net I/σ(I): 5.71
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 1293 / CC1/2: 0.559
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→19.56 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 33.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3024 1018 8.7 %
Rwork0.2486 --
obs0.2533 11707 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 49 40 2404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022425
X-RAY DIFFRACTIONf_angle_d0.4373270
X-RAY DIFFRACTIONf_dihedral_angle_d12.052825
X-RAY DIFFRACTIONf_chiral_restr0.033354
X-RAY DIFFRACTIONf_plane_restr0.003420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.460.343880.3154975X-RAY DIFFRACTION87
2.46-2.560.3768950.30431002X-RAY DIFFRACTION90
2.56-2.680.3354970.30191011X-RAY DIFFRACTION90
2.68-2.820.35181010.29971057X-RAY DIFFRACTION94
2.82-30.31821040.27961069X-RAY DIFFRACTION96
3-3.230.30451040.27221086X-RAY DIFFRACTION97
3.23-3.550.31621050.26321099X-RAY DIFFRACTION97
3.55-4.060.28331060.22011116X-RAY DIFFRACTION98
4.06-5.10.26271050.21031124X-RAY DIFFRACTION99
5.1-100.29241130.22461150X-RAY DIFFRACTION99
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)
14.09555.58411.34218.6302-0.53585.94280.61220.83150.2311.5838-0.89412.376-2.1836-1.86370.02330.67150.18830.21870.5616-0.02780.4833-35.9518-10.8248-5.6638
24.35973.34532.05514.7945-2.11237.0752-0.1335-0.51480.35620.9529-0.2014-0.0999-0.3876-1.10550.16880.6510.07990.08590.27610.09810.5342-31.5278-13.7908-0.6819
39.5631-3.67970.02235.3424-3.85235.48461.14330.5244-0.27940.3011-0.5223-0.22460.7757-0.7953-0.43860.5570.0913-0.0430.3432-0.13470.4474-36.2381-22.0904-7.4311
44.2946-0.03540.12627.18970.71336.2301-0.34150.1427-0.1626-0.16310.48780.53060.69590.0775-0.03340.2943-0.00960.01080.26330.03750.1734-28.065-15.2731-11.5785
58.5398-2.86264.20755.1757-2.77383.5534-0.50540.5740.3223-0.007-0.02711.3959-0.5537-0.00630.55970.3261-0.1899-0.12780.78440.28310.7075-35.2623-12.3391-15.6451
66.746.47382.81826.36723.75648.7995-0.2213-1.0038-2.49311.27060.7985-0.7218-0.720.4308-0.33760.5062-0.00920.03860.3820.12350.7094-14.2198-36.3072-10.3285
78.4202-3.1371-3.62225.65320.59661.95570.40991.21160.5962-2.06560.10620.10831.3887-0.7424-0.49190.8755-0.0668-0.08490.390.14570.4232-19.7674-34.9406-14.5998
87.6997-3.32240.55396.6772-0.91586.84320.186-0.4691-0.681-0.2790.17541.37240.3525-0.1475-0.12740.5033-0.01330.05690.20230.06410.4682-22.9094-34.1011-3.4267
96.74722.5964-3.76931.7845-1.79612.2879-0.0616-0.0509-0.17830.01260.08390.11530.42270.39570.15060.36330.0468-0.05070.280.00270.3333-16.5421-26.2131-7.1178
107.696-7.05432.90278.0570.75218.4249-0.50911.2121-0.8243-0.9905-0.38160.70342.3237-0.81960.65771.0343-0.0587-0.07050.7476-0.15210.1908-25.8826-22.2831-30.1187
118.2322-4.95690.16599.36330.37380.0430.61441.46730.2702-2.1746-0.3934-0.58290.4213-0.5195-0.23560.79320.1611-0.00510.43050.04090.2847-24.8531-14.1764-30.1506
123.6770.25180.39726.90081.1913.8544-0.3045-0.08090.3523-0.66340.34290.8024-0.1057-0.2186-0.10830.211-0.03690.05210.26810.04030.2384-24.3514-17.6675-20.6041
131.61870.18910.16830.0729-0.21921.18780.08371.0381-0.1695-0.4946-0.9380.38930.0009-0.43550.4810.17670.1505-0.09930.7949-0.25030.71-32.8413-20.2217-22.7487
146.2217-1.44921.66193.8752-2.35695.7078-1.0351-0.98541.41660.08850.7011-1.4872-0.29870.72690.11210.79980.10060.13080.3839-0.12790.6119-14.12323.6738-12.1178
150.2585-0.0840.07810.0302-0.02650.02460.1606-0.1353-0.03030.8745-0.08580.1099-0.101-0.1044-0.08790.6481-0.08950.34390.05420.48210.8162-20.98232.2363-13.0686
161.3619-1.9856-1.32325.38565.33296.0025-0.2034-0.0031-0.1723-0.7688-0.28420.1865-0.2472-0.54760.06380.61520.0871-0.0140.17330.10140.3376-15.45851.4182-23.3124
175.9456-0.5172-3.09365.7374-2.44983.20830.0436-0.1951-0.1086-0.3310.2394-0.04020.52920.6318-0.30410.2789-0.0039-0.04980.2470.08150.3238-14.1857-6.5942-14.861
184.284-3.35550.83455.4445-4.13744.4857-0.2327-0.6681.71380.47890.1103-0.701-0.87631.45470.14360.5403-0.1494-0.00360.3983-0.12960.3201-7.2599-2.7466-18.6003
192.287-2.717-1.24218.28174.94153.0535-0.3226-2.1745-0.53882.517-0.1547-0.53150.50711.82790.32110.6603-0.064-0.06410.89830.09210.4366-12.9171-14.39826.9756
203.44410.238-3.39293.9735-0.25193.34430.3909-1.3393-0.19740.29940.0456-1.0041-0.0781-1.468-0.55520.5036-0.0092-0.08330.8318-0.1260.4663-10.1997-9.1063.0909
217.7337-7.014-4.86997.854.5874.50110.1176-0.76551.27750.84080.6028-2.55870.83781.538-0.98190.5732-0.1547-0.21320.9310.07120.7912-3.3643-18.62622.9221
223.8578-2.6188-4.04773.93431.78165.1295-0.0257-0.7912-0.87850.1323-0.04840.0472-0.02030.61790.04040.3571-0.0309-0.06220.26820.08550.3403-13.8542-18.8964-2.2142
232.7429-0.0550.15265.95395.25484.65760.42941.00650.825-3.1108-0.0479-2.5077-2.02650.7475-0.34470.86050.02440.28360.38340.09970.9138-0.7066-17.9658-23.5378
246.60852.46043.29433.56482.1442.6396-0.31930.6272-0.6031-0.0420.668-0.87820.28281.4732-0.27540.29730.03310.03430.4206-0.03150.43011.319-16.9264-15.3136
256.9261-1.3423-0.24954.26271.23147.3638-0.4227-0.09250.1744-0.3756-0.1505-0.247-0.30590.79980.3790.2935-0.01710.0180.1640.07910.183-8.2969-14.3483-16.9973
264.4001-3.8969-4.56858.56730.24228.9422-0.20052.3090.1081-1.97790.1637-0.3933-0.33650.31130.22430.4994-0.17510.14230.6027-0.05630.4747-4.1911-7.658-21.3885
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 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 26 )
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 6 )
11X-RAY DIFFRACTION11chain 'E' and (resid 7 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 6 )
15X-RAY DIFFRACTION15chain 'G' and (resid 7 through 12 )
16X-RAY DIFFRACTION16chain 'G' and (resid 13 through 21 )
17X-RAY DIFFRACTION17chain 'H' and (resid 1 through 22 )
18X-RAY DIFFRACTION18chain 'H' and (resid 23 through 27 )
19X-RAY DIFFRACTION19chain 'I' and (resid 1 through 6 )
20X-RAY DIFFRACTION20chain 'I' and (resid 7 through 12 )
21X-RAY DIFFRACTION21chain 'I' and (resid 13 through 21 )
22X-RAY DIFFRACTION22chain 'J' and (resid 1 through 26 )
23X-RAY DIFFRACTION23chain 'K' and (resid 1 through 6 )
24X-RAY DIFFRACTION24chain 'K' and (resid 7 through 21 )
25X-RAY DIFFRACTION25chain 'L' and (resid 1 through 22 )
26X-RAY DIFFRACTION26chain 'L' and (resid 23 through 28 )

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