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Yorodumi- PDB-6hn4: Leucine-zippered human insulin receptor ectodomain with single bo... -
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-Basic information
Entry | Database: PDB / ID: 6hn4 | |||||||||||||||
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Title | Leucine-zippered human insulin receptor ectodomain with single bound insulin - "lower" membrane-proximal part | |||||||||||||||
Components | Insulin receptor,Insulin receptor,General control protein GCN4 | |||||||||||||||
Keywords | SIGNALING PROTEIN / insulin / insulin receptor ectodomain / signal transdution | |||||||||||||||
Function / homology | Function and homology information regulation of female gonad development / positive regulation of meiotic cell cycle / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / positive regulation of developmental growth / response to amino acid starvation / insulin-like growth factor II binding / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation ...regulation of female gonad development / positive regulation of meiotic cell cycle / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / positive regulation of developmental growth / response to amino acid starvation / insulin-like growth factor II binding / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / nitrogen catabolite activation of transcription from RNA polymerase II promoter / positive regulation of protein-containing complex disassembly / cargo receptor activity / dendritic spine maintenance / PTB domain binding / insulin binding / neuronal cell body membrane / adrenal gland development / Signaling by Insulin receptor / IRS activation / amyloid-beta clearance / activation of protein kinase activity / positive regulation of respiratory burst / regulation of embryonic development / TFIID-class transcription factor complex binding / transport across blood-brain barrier / positive regulation of receptor internalization / amino acid biosynthetic process / insulin receptor substrate binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / phosphatidylinositol 3-kinase binding / heart morphogenesis / dendrite membrane / insulin-like growth factor receptor binding / Insulin receptor recycling / cellular response to amino acid starvation / receptor-mediated endocytosis / neuron projection maintenance / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / learning / caveola / positive regulation of glucose import / positive regulation of MAP kinase activity / memory / receptor internalization / receptor protein-tyrosine kinase / cellular response to growth factor stimulus / RNA polymerase II transcription regulator complex / peptidyl-tyrosine phosphorylation / cellular response to insulin stimulus / male gonad development / cell surface receptor protein tyrosine kinase signaling pathway / protein self-association / positive regulation of nitric oxide biosynthetic process / late endosome / glucose homeostasis / insulin receptor signaling pathway / amyloid-beta binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / positive regulation of MAPK cascade / protein autophosphorylation / lysosome / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / carbohydrate metabolic process / intracellular signal transduction / positive regulation of cell migration / symbiont entry into host cell / G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / axon / protein domain specific binding / external side of plasma membrane / protein phosphorylation / chromatin binding / positive regulation of cell population proliferation / protein-containing complex binding / GTP binding / regulation of DNA-templated transcription Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||
Authors | Weis, F. / Menting, J.G. / Margetts, M.B. / Chan, S.J. / Xu, Y. / Tennagels, N. / Wohlfart, P. / Langer, T. / Mueller, C.W. / Dreyer, M.K. / Lawrence, M.C. | |||||||||||||||
Funding support | Australia, United States, 4items
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Citation | Journal: Nat Commun / Year: 2018 Title: The signalling conformation of the insulin receptor ectodomain. Authors: Felix Weis / John G Menting / Mai B Margetts / Shu Jin Chan / Yibin Xu / Norbert Tennagels / Paulus Wohlfart / Thomas Langer / Christoph W Müller / Matthias K Dreyer / Michael C Lawrence / Abstract: Understanding the structural biology of the insulin receptor and how it signals is of key importance in the development of insulin analogs to treat diabetes. We report here a cryo-electron microscopy ...Understanding the structural biology of the insulin receptor and how it signals is of key importance in the development of insulin analogs to treat diabetes. We report here a cryo-electron microscopy structure of a single insulin bound to a physiologically relevant, high-affinity version of the receptor ectodomain, the latter generated through attachment of C-terminal leucine zipper elements to overcome the conformational flexibility associated with ectodomain truncation. The resolution of the cryo-electron microscopy maps is 3.2 Å in the insulin-binding region and 4.2 Å in the membrane-proximal region. The structure reveals how the membrane proximal domains of the receptor come together to effect signalling and how insulin's negative cooperativity of binding likely arises. Our structure further provides insight into the high affinity of certain super-mitogenic insulins. Together, these findings provide a new platform for insulin analog investigation and design. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6hn4.cif.gz | 156.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hn4.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/6hn4 ftp://data.pdbj.org/pub/pdb/validation_reports/hn/6hn4 | HTTPS FTP |
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-Related structure data
Related structure data | 0246MC 0247C 6hn5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 106728.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: INSR, GCN4, AAS3, ARG9, YEL009C / Plasmid: pEE14 / Strain: ATCC 204508 / S288c / Cell line (production host): Lec8 / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P06213, UniProt: P03069, receptor protein-tyrosine kinase #2: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Leucine zippered human insulin receptor ectodomain (IR-A isoform, "deltabeta" mutant) in complex with insulin and two Fv 83-7 modules : "lower" membrane-proximal part Type: COMPLEX Details: Note: Attached to the leucine-zippered insulin receptor ectodomain are two Fv 83-7 modules. One of these is present within this map volume but it is very poorly ordered and thus left ...Details: Note: Attached to the leucine-zippered insulin receptor ectodomain are two Fv 83-7 modules. One of these is present within this map volume but it is very poorly ordered and thus left completely unmodelled. See the manuscript for further details. Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||
Source (recombinant) | Organism: Cricetulus griseus (Chinese hamster) / Cell: Lec8 / Plasmid: pEE14 | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.094 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 16 sec. / Electron dose: 1.85 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2287 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 20 / Used frames/image: 1-20 |
-Processing
Software | Name: PHENIX / Version: 1.13-2998_1692: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 747074 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98481 / Algorithm: BACK PROJECTION / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4ZXB |