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- PDB-6tc2: Monoclinic human insulin in complex with p-coumaric acid -

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Basic information

Entry
Database: PDB / ID: 6tc2
TitleMonoclinic human insulin in complex with p-coumaric acid
ComponentsInsulin
KeywordsHORMONE / HUMAN INSULIN / p-coumaric acid / HEXAMER / COMPLEX
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic 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 / Insulin processing / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic 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 / Insulin processing / regulation of protein secretion / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / PHOSPHATE ION / THIOCYANATE ION / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsTriandafillidis, D.-P. / Parthenios, N. / Spiliopoulou, M. / Valmas, A. / Kosinas, C. / Gozzo, F. / Reinle-Schmitt, M. / Beckers, D. / Degen, T. / Pop, M. ...Triandafillidis, D.-P. / Parthenios, N. / Spiliopoulou, M. / Valmas, A. / Kosinas, C. / Gozzo, F. / Reinle-Schmitt, M. / Beckers, D. / Degen, T. / Pop, M. / Fitch, A. / Wollenhaupt, J. / Weiss, M.S. / Karavassili, F. / Margiolaki, I.
Funding support Greece, 2items
OrganizationGrant numberCountry
General Secretariat for Research and Technology Greece
Hellenic Foundation for Research and Innovation3051 Greece
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Insulin polymorphism induced by two polyphenols: new crystal forms and advances in macromolecular powder diffraction.
Authors: Triandafillidis, D.P. / Parthenios, N. / Spiliopoulou, M. / Valmas, A. / Kosinas, C. / Gozzo, F. / Reinle-Schmitt, M. / Beckers, D. / Degen, T. / Pop, M. / Fitch, A.N. / Wollenhaupt, J. / ...Authors: Triandafillidis, D.P. / Parthenios, N. / Spiliopoulou, M. / Valmas, A. / Kosinas, C. / Gozzo, F. / Reinle-Schmitt, M. / Beckers, D. / Degen, T. / Pop, M. / Fitch, A.N. / Wollenhaupt, J. / Weiss, M.S. / Karavassili, F. / Margiolaki, I.
History
DepositionNov 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin
B: Insulin
C: Insulin
D: Insulin
E: Insulin
F: Insulin
G: Insulin
H: Insulin
I: Insulin
J: Insulin
K: Insulin
L: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,17323
Polymers143,87812
Non-polymers1,29511
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20400 Å2
ΔGint-228 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.000, 67.650, 47.590
Angle α, β, γ (deg.)90.000, 94.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Insulin


Mass: 11989.862 Da / Num. of mol.: 12
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

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.94 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 5.82
Details: 12.78 mg/mL insulin, 0.77 mM zinc acetate, 40 mM p-coumaric acid, 3.2%(w/v) PEG-1000, 10 mM sodium thiocyanate, 0.4 M phosphate mixture (Na2HPO4, KH2PO4), pH = 5.82

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.36→47.423 Å / Num. obs: 54569 / % possible obs: 98.2 % / Redundancy: 12.727 % / Biso Wilson estimate: 26.592 Å2 / CC1/2: 1 / Rrim(I) all: 0.063 / Χ2: 1.061 / Net I/σ(I): 18.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.36-1.428.3091.8890.9559080.3672.01287.7
1.42-1.511.9881.181.9372220.6861.23298.3
1.5-1.6113.5770.6893.7178900.9050.715100
1.61-1.7413.1890.3746.6369230.9650.38999.8
1.74-1.913.7680.21311.7461490.9890.221100
1.9-2.1313.2950.11121.3159210.9970.11599.9
2.13-2.4513.8360.07233.6749500.9990.075100
2.45-313.4830.05246.343530.9990.05499.8
3-4.2413.260.03659.633680.9990.03799.6
4.24-47.42313.3680.03266.06188510.03399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.7-3644refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EV6

1ev6


Resolution: 1.36→47.423 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1877 --
Rwork0.1601 --
obs-54568 98.2 %
Displacement parametersBiso max: 133.54 Å2 / Biso mean: 34.3236 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: LAST / Resolution: 1.36→47.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 80 189 2607

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