+Open data
-Basic information
Entry | Database: PDB / ID: 4oga | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Insulin in complex with Site 1 of the human insulin receptor | |||||||||
Components |
| |||||||||
Keywords | HORMONE RECEPTOR/HORMONE/IMMUNE SYSTEM / CELL SURFACE RECEPTOR/IMMUNE SYSTEM / INSULIN RECEPTOR / CT PEPTIDE / INSULIN / HORMONE RECEPTOR-HORMONE-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information 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 / PTB domain binding / insulin binding / negative regulation of NAD(P)H oxidase activity / neuronal cell body membrane / adrenal gland development / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / negative regulation of fatty acid metabolic process / nitric oxide-cGMP-mediated signaling / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / amyloid-beta clearance / positive regulation of peptide hormone secretion / activation of protein kinase activity / Regulation of gene expression in beta cells / positive regulation of respiratory burst / regulation of embryonic development / transport across blood-brain barrier / positive regulation of receptor internalization / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / insulin receptor substrate binding / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / epidermis development / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / regulation of protein localization to plasma membrane / positive regulation of nitric oxide mediated signal transduction / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / phosphatidylinositol 3-kinase binding / heart morphogenesis / 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 / transport vesicle / positive regulation of protein autophosphorylation / dendrite membrane / insulin-like growth factor receptor binding / Insulin receptor recycling / receptor-mediated endocytosis / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / learning / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / caveola / endosome lumen / positive regulation of cytokine production / acute-phase response / regulation of transmembrane transporter activity / positive regulation of protein secretion / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / positive regulation of MAP kinase activity / memory / insulin receptor binding / cognition / negative regulation of protein catabolic process / receptor internalization / positive regulation of neuron projection development / hormone activity / receptor protein-tyrosine kinase / vasodilation / Golgi lumen / cellular response to growth factor stimulus / positive regulation of protein localization to nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Lawrence, M.C. / Menting, J.G. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Protective hinge in insulin opens to enable its receptor engagement. Authors: Menting, J.G. / Yang, Y. / Chan, S.J. / Phillips, N.B. / Smith, B.J. / Whittaker, J. / Wickramasinghe, N.P. / Whittaker, L.J. / Pandyarajan, V. / Wan, Z.L. / Yadav, S.P. / Carroll, J.M. / ...Authors: Menting, J.G. / Yang, Y. / Chan, S.J. / Phillips, N.B. / Smith, B.J. / Whittaker, J. / Wickramasinghe, N.P. / Whittaker, L.J. / Pandyarajan, V. / Wan, Z.L. / Yadav, S.P. / Carroll, J.M. / Strokes, N. / Roberts, C.T. / Ismail-Beigi, F. / Milewski, W. / Steiner, D.F. / Chauhan, V.S. / Ward, C.W. / Weiss, M.A. / Lawrence, M.C. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4oga.cif.gz | 258.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4oga.ent.gz | 213.3 KB | Display | PDB format |
PDBx/mmJSON format | 4oga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/4oga ftp://data.pdbj.org/pub/pdb/validation_reports/og/4oga | HTTPS FTP |
---|
-Related structure data
Related structure data | 2mliC 2mpiC 4nibC 3w11S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein/peptide , 2 types, 2 molecules AB
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 1 / Fragment: UNP residues 90-110 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 | Mass: 3433.953 Da / Num. of mol.: 1 / Fragment: UNP residues 25-54 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 |
-Insulin receptor ... , 2 types, 2 molecules EF
#5: Protein | Mass: 36231.762 Da / Num. of mol.: 1 / Fragment: L1-CR, UNP residues 28-377 Source method: isolated from a genetically manipulated source Details: Lec 8 mutant CHO cell / Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Cell line (production host): Lec 8 mutant CHO cell / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06213 |
---|---|
#6: Protein/peptide | Mass: 1922.143 Da / Num. of mol.: 1 / Fragment: alpha-CT peptide, UNP residues 731-746 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P06213 |
-Antibody , 2 types, 2 molecules CD
#3: Antibody | Mass: 12886.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Hybridoma cell / Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma cell / Production host: mus musculus (house mouse) |
---|---|
#4: Antibody | Mass: 12684.292 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Hybridoma cell / Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma cell / Production host: mus musculus (house mouse) |
-Sugars , 3 types, 5 molecules
#7: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose 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: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 5.79 Å3/Da / Density % sol: 78.75 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.9-1.1M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE-HCL, 0.02% SODIUM AZIDE, PH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||||||||
Detector |
| ||||||||||||||||||||||||
Radiation |
| ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 3.5→20 Å / Num. all: 20608 / Num. obs: 20361 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 38.7 % / Biso Wilson estimate: 191.63 Å2 / Rmerge(I) obs: 0.214 / Net I/σ(I): 12.1 | ||||||||||||||||||||||||
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 32.6 % / Rmerge(I) obs: 14.8 / Mean I/σ(I) obs: 0.17 / Num. unique all: 1609 / % possible all: 96.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3W11 Resolution: 3.5→19.78 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9193 / SU R Cruickshank DPI: 3.609 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 238.45 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 1.177 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→19.78 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.69 Å / Total num. of bins used: 10
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|