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Yorodumi- EMDB-30231: Cryo-EM Structure for the Ectodomain of the Full-length Human Ins... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30231 | |||||||||
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Title | Cryo-EM Structure for the Ectodomain of the Full-length Human Insulin Receptor in Complex with 2 Insulin | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information cellular response to oxygen-containing compound / 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 ...cellular response to oxygen-containing compound / 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 / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / PTB domain binding / adrenal gland development / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / activation of protein kinase activity / IRS activation / Insulin processing / neuronal cell body membrane / 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 / positive regulation of receptor internalization / amyloid-beta clearance / alpha-beta T cell activation / transport across blood-brain barrier / regulation of embryonic development / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / insulin receptor substrate binding / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / epidermis development / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of gluconeogenesis / Signal attenuation / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / phosphatidylinositol 3-kinase binding / heart morphogenesis / positive regulation of lipid biosynthetic process / positive regulation of insulin receptor signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / nitric oxide-cGMP-mediated signaling / positive regulation of protein autophosphorylation / transport vesicle / insulin-like growth factor receptor binding / Insulin receptor recycling / dendrite membrane / 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 / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / receptor-mediated endocytosis / positive regulation of nitric-oxide synthase activity / learning / acute-phase response / positive regulation of cytokine production / cognition / positive regulation of long-term synaptic potentiation / Regulation of insulin secretion / endosome lumen / positive regulation of D-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 / positive regulation of MAP kinase activity / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / hormone activity / caveola / regulation of synaptic plasticity / receptor internalization / cellular response to growth factor stimulus / positive regulation of neuron projection development / memory / positive regulation of protein localization to nucleus / Golgi lumen Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Yu D / Zhang X / Sun J / Li X / Wu Z / Han X / Fan C / Ma Y / Ouyang Q / Wang T | |||||||||
Citation | Journal: To Be Published Title: Insulin Binding Induced the Ectodomain Conformational Dynamics in the Full-length Human Insulin Receptor Authors: Yu D / Zhang X / Sun J / Li X / Wu Z / Han X / Fan C / Ma Y / Ouyang Q / Wang T | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30231.map.gz | 2.1 MB | EMDB map data format | |
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Header (meta data) | emd-30231-v30.xml emd-30231.xml | 24.6 KB 24.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30231_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_30231.png | 151.8 KB | ||
Others | emd_30231_half_map_1.map.gz emd_30231_half_map_2.map.gz | 11.8 MB 11.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30231 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30231 | HTTPS FTP |
-Validation report
Summary document | emd_30231_validation.pdf.gz | 543.6 KB | Display | EMDB validaton report |
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Full document | emd_30231_full_validation.pdf.gz | 543.2 KB | Display | |
Data in XML | emd_30231_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_30231_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30231 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30231 | HTTPS FTP |
-Related structure data
Related structure data | 7bwaMC 7bw7C 7bw8C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30231.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_30231_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_30231_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human Insulin Receptor Complexed with 1 Insulin
Entire | Name: Human Insulin Receptor Complexed with 1 Insulin |
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Components |
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-Supramolecule #1: Human Insulin Receptor Complexed with 1 Insulin
Supramolecule | Name: Human Insulin Receptor Complexed with 1 Insulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 |
Molecular weight | Theoretical: 130 KDa |
-Supramolecule #2: Insulin Receptor
Supramolecule | Name: Insulin Receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Supramolecule #3: Insulin
Supramolecule | Name: Insulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Insulin receptor
Macromolecule | Name: Insulin receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 154.114516 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: HLYPGEVCPG MDIRNNLTRL HELENCSVIE GHLQILLMFK TRPEDFRDLS FPKLIMITDY LLLFRVYGLE SLKDLFPNLT VIRGSRLFF NYALVIFEMV HLKELGLYNL MNITRGSVRI EKNNELCYLA TIDWSRILDS VEDNYIVLNK DDNEECGDIC P GTAKGKTN ...String: HLYPGEVCPG MDIRNNLTRL HELENCSVIE GHLQILLMFK TRPEDFRDLS FPKLIMITDY LLLFRVYGLE SLKDLFPNLT VIRGSRLFF NYALVIFEMV HLKELGLYNL MNITRGSVRI EKNNELCYLA TIDWSRILDS VEDNYIVLNK DDNEECGDIC P GTAKGKTN CPATVINGQF VERCWTHSHC QKVCPTICKS HGCTAEGLCC HSECLGNCSQ PDDPTKCVAC RNFYLDGRCV ET CPPPYYH FQDWRCVNFS FCQDLHHKCK NSRRQGCHQY VIHNNKCIPE CPSGYTMNSS NLLCTPCLGP CPKVCHLLEG EKT IDSVTS AQELRGCTVI NGSLIINIRG GNNLAAELEA NLGLIEEISG YLKIRRSYAL VSLSFFRKLR LIRGETLEIG NYSF YALDN QNLRQLWDWS KHNLTITQGK LFFHYNPKLC LSEIHKMEEV SGTKGRQERN DIALKTNGDQ ASCENELLKF SYIRT SFDK ILLRWEPYWP PDFRDLLGFM LFYKEAPYQN VTEFDGQDAC GSNSWTVVDI DPPLRSNDPK SQNHPGWLMR GLKPWT QYA IFVKTLVTFS DERRTYGAKS DIIYVQTDAT NPSVPLDPIS VSNSSSQIIL KWKPPSDPNG NITHYLVFWE RQAEDSE LF ELDYCLKGLK LPSRTWSPPF ESEDSQKHNQ SEYEDSAGEC CSCPKTDSQI LKELEESSFR KTFEDYLHNV VFVPRKTS S GTGAEDPRPS RKRRSLGDVG NVTVAVPTVA AFPNTSSTSV PTSPEEHRPF EKVVNKESLV ISGLRHFTGY RIELQACNQ DTPEERCSVA AYVSARTMPE AKADDIVGPV THEIFENNVV HLMWQEPKEP NGLIVLYEVS YRRYGDEELH LCVSRKHFAL ERGCRLRGL SPGNYSVRIR ATSLAGNGSW TEPTYFYVTD YLDVPSNIAK IIIGPLIFVF LFSVVIGSIY LFLRKRQPDG P LGPLYASS NPEYLSASDV FPCSVYVPDE WEVSREKITL LRELGQGSFG MVYEGNARDI IKGEAETRVA VKTVNESASL RE RIEFLNE ASVMKGFTCH HVVRLLGVVS KGQPTLVVME LMAHGDLKSY LRSLRPEAEN NPGRPPPTLQ EMIQMAAEIA DGM AYLNAK KFVHRDLAAR NCMVAHDFTV KIGDFGMTRD IYETDYYRKG GKGLLPVRWM APESLKDGVF TTSSDMWSFG VVLW EITSL AEQPYQGLSN EQVLKFVMDG GYLDQPDNCP ERVTDLMRMC WQFNPKMRPT FLEIVNLLKD DLHPSFPEVS FFHSE ENKA PESEELEMEF EDMENVPLDR SSHCQREEAG GRDGGSSLGF KRSYEEHIPY THMNGGKKNG RILTLPRSNP S |
-Macromolecule #2: Insulin fusion
Macromolecule | Name: Insulin fusion / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.380529 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: FVNQHLCGSH LVEALYLVCG ERGFFYTPKT RREAEDLQGS LQPLALEGSL QKRGIVEQCC TSICSLYQLE NYCN |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK III | |||||||||||||||
Details | The sample was prepared using the gradient fixation method. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 5 / Number real images: 17122 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 Details: Images were collected in movie mode with 40 frames per 10 seconds. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.7000000000000001 µm / Calibrated magnification: 43796 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 255 / Target criteria: Correlation coefficient | ||||||||||
Output model | PDB-7bwa: |