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- PDB-6vep: Human insulin in complex with the human insulin microreceptor in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vep | |||||||||
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Title | Human insulin in complex with the human insulin microreceptor in turn in complex with Fv 83-7 | |||||||||
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![]() | HORMONE RECEPTOR/HORMONE/IMMUNE SYSTEM / HORMONE / HORMONE RECEPTOR-HORMONE-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() regulation of female gonad development / positive regulation of meiotic cell cycle / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly ...regulation of female gonad development / positive regulation of meiotic cell cycle / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / cargo receptor activity / dendritic spine maintenance / insulin binding / PTB domain binding / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / adrenal gland development / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / neuronal cell body membrane / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / activation of protein kinase activity / Insulin processing / regulation of protein secretion / amyloid-beta clearance / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / positive regulation of receptor internalization / alpha-beta T cell activation / regulation of embryonic development / negative regulation of respiratory burst involved in inflammatory response / transport across blood-brain barrier / insulin receptor substrate binding / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / epidermis development / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / phosphatidylinositol 3-kinase binding / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / heart morphogenesis / 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 / dendrite membrane / 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 / receptor-mediated endocytosis / learning / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / caveola / Regulation of insulin secretion / acute-phase response / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of cell differentiation / negative regulation of proteolysis / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / positive regulation of MAP kinase activity / wound healing / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / receptor internalization / receptor protein-tyrosine kinase / memory / cellular response to growth factor stimulus / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / peptidyl-tyrosine phosphorylation Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lawrence, M.C. / Menting, J.G.T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A structurally minimized yet fully active insulin based on cone-snail venom insulin principles. Authors: Xiong, X. / Menting, J.G. / Disotuar, M.M. / Smith, N.A. / Delaine, C.A. / Ghabash, G. / Agrawal, R. / Wang, X. / He, X. / Fisher, S.J. / MacRaild, C.A. / Norton, R.S. / Gajewiak, J. / ...Authors: Xiong, X. / Menting, J.G. / Disotuar, M.M. / Smith, N.A. / Delaine, C.A. / Ghabash, G. / Agrawal, R. / Wang, X. / He, X. / Fisher, S.J. / MacRaild, C.A. / Norton, R.S. / Gajewiak, J. / Forbes, B.E. / Smith, B.J. / Safavi-Hemami, H. / Olivera, B. / Lawrence, M.C. / Chou, D.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 970.5 KB | Display | ![]() |
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PDB format | ![]() | 817.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 995 KB | Display | ![]() |
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Full document | ![]() | 1002.6 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6veqC ![]() 6vetC ![]() 4ogaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein/peptide , 2 types, 8 molecules AGMSBHNT
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Insulin receptor subunit ... , 2 types, 8 molecules EKQWFLRX
#5: Protein | Mass: 36231.762 Da / Num. of mol.: 4 / Fragment: residues 28-337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P06213, receptor protein-tyrosine kinase #6: Protein/peptide | Mass: 1922.143 Da / Num. of mol.: 4 / Fragment: residues 731-746 / Source method: obtained synthetically / Source: (synth.) ![]() References: UniProt: P06213, receptor protein-tyrosine kinase |
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-Antibody , 2 types, 8 molecules CIOUDJPV
#3: Antibody | Mass: 15058.748 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Antibody | Mass: 13367.913 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 7 types, 20 molecules ![](data/chem/img/NAG.gif)
#7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #11: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #12: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #13: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 18 molecules ![](data/chem/img/HOH.gif)
#14: Water | ChemComp-HOH / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.01 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: Protein: 4.5 mg/ml in 10 mM HEPES pH 7.5 Well condition: 16% PEG 3350, 0.2 M sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 83231 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 83.57 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.263 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 3.64 / Mean I/σ(I) obs: 0.44 / Num. unique obs: 4086 / CC1/2: 0.112 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OGA Resolution: 2.9→48.89 Å / Cor.coef. Fo:Fc: 0.9012 / Cor.coef. Fo:Fc free: 0.8787 / SU R Cruickshank DPI: 1.071 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.812 / SU Rfree Blow DPI: 0.305 / SU Rfree Cruickshank DPI: 0.316
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Displacement parameters | Biso mean: 101.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.552 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→48.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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