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- PDB-9qld: Rhombohedral crystalline form of human insulin complexed with m-n... -

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Basic information

Entry
Database: PDB / ID: 9qld
TitleRhombohedral crystalline form of human insulin complexed with m-nitrophenol
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / insulin complex / m-nitrophenol / rhombohedral / HI
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
ACETATE ION / THIOCYANATE ION / 3-nitrophenol / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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
DepositionMar 20, 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)12,16110
Polymers11,6354
Non-polymers5266
Water543
1
A: Insulin A chain
B: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0805
Polymers5,8182
Non-polymers2633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0815
Polymers5,8182
Non-polymers2643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.932, 78.932, 39.197
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11B-101-

SCN

21B-101-

SCN

31B-101-

SCN

41B-102-

ZN

51D-101-

ZN

61D-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 or (resid 2 and (name...
d_2ens_1(chain "C" and (resid 1 through 3 or (resid 4...
d_1ens_2(chain "B" and (resid 1 through 21 or (resid 22...
d_2ens_2(chain "D" and resid 1 through 28)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYCYSCYSAA1 - 71 - 7
d_12ens_1SERSERASNASNAA9 - 219 - 21
d_21ens_1GLYGLYCYSCYSCC1 - 71 - 7
d_22ens_1SERSERASNASNCC9 - 219 - 21
d_11ens_2PHEPHEPROPROBB1 - 281 - 28
d_21ens_2PHEPHEPROPRODD1 - 281 - 28

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.0140346823908, -0.999222831332, 0.0368342372698), (-0.999846736607, 0.0144099603784, 0.00994265249085), (-0.0104657052725, -0.0366890499598, -0.999271926267)-1.18339802491, -0.613758634389, 0.208549351433
2given(0.0887492868941, -0.995906435638, -0.0171445481464), (-0.995878148891, -0.0890438924739, 0.0172597153946), (-0.0187156789405, 0.0155420934384, -0.99970403955)0.288638591764, 0.188308662531, 0.294661411014

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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, 9 molecules

#3: Chemical ChemComp-ZCQ / 3-nitrophenol


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3 / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.03 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 294.15 K / Method: batch mode / pH: 7.5
Details: 12.78 mg/mL human insulin, 0.77 mM zinc acetate, 40.06 mM m-nitrophenol, 10.09 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: Nov 13, 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: 2.55→39.47 Å / Num. obs: 2966 / % possible obs: 99.4 % / Redundancy: 2 % / Biso Wilson estimate: 74.56 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.048 / Χ2: 1.07 / Net I/σ(I): 15.2
Reflection shellResolution: 2.55→2.67 Å / Redundancy: 2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 379 / CC1/2: 0.618 / Rrim(I) all: 0.435 / Χ2: 0.58 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→39.47 Å / SU ML: 0.2166 / Cross valid method: FREE R-VALUE / σ(F): 2.08 / Phase error: 18.6473
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 169 5.7 %
Rwork0.1906 2796 -
obs0.1937 2965 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.73 Å2
Refinement stepCycle: LAST / Resolution: 2.55→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 29 3 752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034766
X-RAY DIFFRACTIONf_angle_d0.56571040
X-RAY DIFFRACTIONf_chiral_restr0.0393119
X-RAY DIFFRACTIONf_plane_restr0.0037134
X-RAY DIFFRACTIONf_dihedral_angle_d20.1193240
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.648679886561
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.09709066243
LS refinement shellResolution: 2.55→39.47 Å
RfactorNum. reflection% reflection
Rfree0.2403 169 -
Rwork0.1906 2796 -
obs--99.43 %

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