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- PDB-9ibb: Rhombohedral crystalline form of human insulin complexed with m-cresol -

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Basic information

Entry
Database: PDB / ID: 9ibb
TitleRhombohedral crystalline form of human insulin complexed with m-cresol
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / Human Insulin / m-cresol / ligand complex / R6 conformation / polymorph
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
M-CRESOL / THIOCYANATE ION / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsPapaefthymiou, C. / Nanao, M.H. / Margiolaki, I. / Kontarinis, A. / Kafetzi, S. / Konstantopoulos, M. / Koutoulas, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Appl.Crystallogr. / Year: 2025
Title: Exploring humidity effects on polycrystalline human insulin ligand complexes:preliminary crystallographic insights
Authors: Kontarinis, A. / Papaefthymiou, C. / Kafetzi, S. / Konstantopoulos, M. / Koutoulas, D. / Nanao, M.H. / Margiolaki, I.
History
DepositionFeb 12, 2025Deposition site: PDBE / Processing site: PDBE
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,13310
Polymers11,6354
Non-polymers4976
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-85 kcal/mol
Surface area6180 Å2
Unit cell
Length a, b, c (Å)78.684, 78.684, 39.883
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-101-

SCN

21B-101-

SCN

31B-101-

SCN

41B-102-

ZN

51D-101-

ZN

61D-206-

HOH

71D-210-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A1 - 21
211A1 - 21
322A2 - 27
422A2 - 27

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide Insulin A 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: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE MISSING AMINO ACIDS WERE NOT INCLUDED IN THE PDB FILE BECAUSE THERE WAS NO ELECTRON DENSITY IN THE CORRESPONDING POSITION
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308

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Non-polymers , 5 types, 37 molecules

#3: Chemical ChemComp-CRS / M-CRESOL


Mass: 108.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 294.15 K / Method: batch mode / pH: 7.5
Details: 13.14 mg/mL human insulin, 0.80 mM zinc acetate, 0.51% v/v m-cresol in ethanol, 10.25 mM sodium thiocyanate, 0.4 M sodium-monopotassium phosphate mixture

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 7, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.84→39.342 Å / Num. obs: 7990 / % possible obs: 99.9 % / Redundancy: 1.99 % / Biso Wilson estimate: 36.419 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Rrim(I) all: 0.071 / Χ2: 0.72 / Net I/σ(I): 5.6
Reflection shellResolution: 1.84→1.88 Å / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 503 / CC1/2: 0.627 / Rpim(I) all: 0.408 / Rrim(I) all: 0.577 / Χ2: 0.63 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→39.342 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.819 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2239 408 5.108 %
Rwork0.1779 7580 -
all0.18 --
obs-7988 99.85 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.537 Å2
Baniso -1Baniso -2Baniso -3
1--0.113 Å2-0.057 Å2-0 Å2
2---0.113 Å20 Å2
3---0.368 Å2
Refinement stepCycle: LAST / Resolution: 1.84→39.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 27 31 806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.012795
X-RAY DIFFRACTIONr_bond_other_d0.0010.016683
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.8191075
X-RAY DIFFRACTIONr_angle_other_deg0.7051.6951571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.253593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.04552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33310113
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.371035
X-RAY DIFFRACTIONr_chiral_restr0.1050.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02189
X-RAY DIFFRACTIONr_nbd_refined0.210.2182
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.2619
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2414
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.219
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.226
X-RAY DIFFRACTIONr_nbd_other0.2120.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5030.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0590.28
X-RAY DIFFRACTIONr_mcbond_it4.2893.344385
X-RAY DIFFRACTIONr_mcbond_other4.2843.346385
X-RAY DIFFRACTIONr_mcangle_it5.0925.98473
X-RAY DIFFRACTIONr_mcangle_other5.1025.988474
X-RAY DIFFRACTIONr_scbond_it4.9473.804410
X-RAY DIFFRACTIONr_scbond_other4.9483.812410
X-RAY DIFFRACTIONr_scangle_it6.7946.869602
X-RAY DIFFRACTIONr_scangle_other6.7886.874603
X-RAY DIFFRACTIONr_lrange_it8.10336.807927
X-RAY DIFFRACTIONr_lrange_other8.06736.815927
X-RAY DIFFRACTIONr_ncsr_local_group_10.1420.05549
X-RAY DIFFRACTIONr_ncsr_local_group_20.1390.05654
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.141860.05007
12AX-RAY DIFFRACTIONLocal ncs0.141860.05007
23AX-RAY DIFFRACTIONLocal ncs0.138790.05006
24AX-RAY DIFFRACTIONLocal ncs0.138790.05006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.84-1.8880.323360.2665620.2696020.9360.95599.33550.27
1.888-1.9390.365160.2885490.295680.9280.94299.47180.287
1.939-1.9950.313300.2115270.2165580.9410.97299.82080.214
1.995-2.0570.265160.1975460.1995620.9570.9751000.2
2.057-2.1240.173160.2085000.2075160.9750.9741000.216
2.124-2.1980.222390.2024740.2045130.9680.9761000.213
2.198-2.2810.295130.2144710.2174860.9490.9799.58850.229
2.281-2.3740.295360.2024330.2094700.9480.97599.78720.225
2.374-2.4790.264270.1784330.1834600.9650.981000.202
2.479-2.5990.282150.1974140.24290.940.9781000.234
2.599-2.7390.137160.1593930.1584090.9880.9841000.194
2.739-2.9050.225290.1653620.173910.970.9821000.205
2.905-3.1040.223260.1943460.1963720.9640.9751000.242
3.104-3.3510.381190.2013260.213450.9070.9751000.237
3.351-3.6680.243170.1662950.173120.9660.9841000.212
3.668-4.0970.251180.1442580.1512760.9710.9881000.179
4.097-4.7220.144100.1452500.1452600.9920.9881000.185
4.722-5.7620.168150.1841970.1832120.9820.9831000.241
5.762-8.0630.1190.1931570.1871660.9910.9781000.267
8.063-39.3420.19250.141860.144920.9790.9898.9130.175
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)
15.81281.36691.87723.4937-0.72348.43390.0917-0.416-0.01420.1983-0.20320.3280.1946-0.19820.11150.05740.02980.02820.0875-0.00920.0621-16.15372.56829.2378
26.8247-0.73642.55434.09560.24074.738-0.1246-0.12120.3051-0.08160.01210.115-0.4682-0.03350.11250.05050.0034-0.00480.0210.00670.0274-9.78355.83074.056
36.54360.9412-3.25125.30741.11225.7357-0.1720.29520.3788-0.3632-0.0140.2141-0.2537-0.22020.18590.11070.0385-0.00160.03680.03290.079-2.657815.9588-8.6617
45.21330.10021.25986.53723.51236.00480.00540.01370.2072-0.2306-0.12710.4861-0.2656-0.49630.12170.040.01910.00360.05110.01120.0596-6.49969.8059-3.3605
Refinement TLS groupSelection: ALL

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