+Open data
-Basic information
Entry | Database: PDB / ID: 7qac | |||||||||
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Title | The T2 structure of polycrystalline cubic human insulin | |||||||||
Components |
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Keywords | HORMONE / cubic / human / insulin / T2 | |||||||||
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 / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / 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 / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / 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 / regulation of cellular amino acid metabolic process / 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 / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / 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 / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / vasodilation / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / glucose metabolic process / regulation of protein localization / glucose homeostasis / insulin receptor signaling pathway / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / Golgi membrane / endoplasmic reticulum lumen / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | POWDER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | |||||||||
Authors | Karavassili, F. / Triandafillidis, D.P. / Valmas, A. / Spiliopoulou, M. / Fili, S. / Kontou, P. / Bowler, M.W. / Von Dreele, R.B. / Fitch, A. / Margiolaki, I. | |||||||||
Funding support | European Union, Greece, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: The T 2 structure of polycrystalline cubic human insulin. Authors: Triandafillidis, D.P. / Karavassili, F. / Spiliopoulou, M. / Valmas, A. / Athanasiadou, M. / Nikolaras, G. / Fili, S. / Kontou, P. / Bowler, M.W. / Chasapis, C.T. / Von Dreele, R.B. / Fitch, ...Authors: Triandafillidis, D.P. / Karavassili, F. / Spiliopoulou, M. / Valmas, A. / Athanasiadou, M. / Nikolaras, G. / Fili, S. / Kontou, P. / Bowler, M.W. / Chasapis, C.T. / Von Dreele, R.B. / Fitch, A.N. / Margiolaki, I. | |||||||||
History |
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Remark 1 | REMARK 250 REFINEMENT. REMARK 250 PROGRAM : GSAS REMARK 250 AUTHORS : LARSON & VON DREELE REMARK ... REMARK 250 REFINEMENT. REMARK 250 PROGRAM : GSAS REMARK 250 AUTHORS : LARSON & VON DREELE REMARK 250 REMARK 250 DATA USED IN REFINEMENT REMARK 250 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 250 RESOLUTION RANGE LOW (ANGSTROMS) : 39.43 REMARK 250 POWDER DIFFRACTION DATA. REMARK 250 REMARK 250 FIT TO DATA USED IN REFINEMENT REMARK 250 NUMBER OF POWDER PATTERNS : 6 REMARK 250 PROFILE R VALUES (%) : 7.70 11.54 12.16 8.80 7.61 2.12 REMARK 250 WEIGHTED PROFILE R VALUES (%) : 10.98 14.75 15.17 12.12 10.95 3.34 REMARK 250 F**2 R VALUES (%) : 42.02 38.68 44.09 38.89 35.52 24.00 REMARK 250 NUMBERS OF POWDER PATTERN POINTS : 8256 7003 7002 7002 7002 4740 REMARK 250 NUMBERS OF REFLECTIONS : 3816 2345 2349 2345 2305 4998 REMARK 250 TOTAL NUMBER OF POWDER POINTS : 41005 REMARK 250 REMARK 250 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 250 PROTEIN ATOMS : REMARK 250 NUCLEIC ACID ATOMS : REMARK 250 HETEROGEN ATOMS : REMARK 250 SOLVENT ATOMS : REMARK 250 REMARK 250 MODEL REFINEMENT. REMARK 250 NUMBER OF LEAST-SQUARES PARAMETERS : 786 REMARK 250 NUMBER OF RESTRAINTS : 1951 REMARK 250 LEAST-SQUARES MATRIX BAND WIDTH : 50 REMARK 250 MARQUARDT COEFFICIENT : 8.30 REMARK 250 REMARK 250 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. NUMBER. REMARK 250 INTERATOMIC DISTANCES (A) :0.015 506 REMARK 250 BOND ANGLES (DEG) : 1.43 702 REMARK 250 CHIRAL VOLUMES (A**3) :0.036 52 REMARK 250 TORSION ANGLE RESTRAINTS (E) : 1.00 98 REMARK 250 DISTANCES FROM RESTRAINT PLANES (A) :0.020 149 REMARK 250 TORSION PSEUDOPOTENTIAL RESTRAINTS (E) : 3.84 68 REMARK 250 ANTI-BUMPING DISTANCE RESTRAINTS (A) :0.123 186 REMARK 250 HYDROGEN BOND DISTANCE RESTRAINTS (A) :0.293 212 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qac.cif.gz | 24.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qac.ent.gz | 10.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qac_validation.pdf.gz | 347.2 KB | Display | wwPDB validaton report |
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Full document | 7qac_full_validation.pdf.gz | 352.7 KB | Display | |
Data in XML | 7qac_validation.xml.gz | 3.4 KB | Display | |
Data in CIF | 7qac_validation.cif.gz | 4.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/7qac ftp://data.pdbj.org/pub/pdb/validation_reports/qa/7qac | HTTPS FTP |
-Related structure data
Related structure data | 9insS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 1 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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#2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 1 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 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: POWDER DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal |
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Crystal grow |
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