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Yorodumi- EMDB-30229: Cryo-EM Structure for the Ectodomain of the Full-length Human Ins... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30229 | |||||||||
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Title | Cryo-EM Structure for the Ectodomain of the Full-length Human Insulin Receptor in Complex with 1 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 / insulin-like growth factor II binding / positive regulation of developmental growth / 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 / insulin-like growth factor II binding / positive regulation of developmental growth / 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 / 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 / IRS activation / activation of protein kinase activity / Insulin processing / neuronal cell body membrane / regulation of protein secretion / amyloid-beta clearance / 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 / alpha-beta T cell activation / regulation of embryonic development / regulation of cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / insulin receptor substrate binding / transport across blood-brain barrier / 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 / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / phosphatidylinositol 3-kinase binding / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / heart morphogenesis / 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 / 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 / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / positive regulation of MAP kinase activity / positive regulation of nitric-oxide synthase activity / learning / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / caveola / 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 / receptor protein-tyrosine kinase / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / peptidyl-tyrosine phosphorylation / regulation of synaptic plasticity / vasodilation / hormone activity / cellular response to insulin stimulus / receptor internalization / memory / cognition / cellular response to growth factor stimulus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 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_30229.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-30229-v30.xml emd-30229.xml | 25.5 KB 25.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30229_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_30229.png | 130.5 KB | ||
Others | emd_30229_half_map_1.map.gz emd_30229_half_map_2.map.gz | 11.7 MB 11.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30229 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30229 | HTTPS FTP |
-Validation report
Summary document | emd_30229_validation.pdf.gz | 502.6 KB | Display | EMDB validaton report |
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Full document | emd_30229_full_validation.pdf.gz | 502.1 KB | Display | |
Data in XML | emd_30229_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_30229_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30229 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30229 | HTTPS FTP |
-Related structure data
Related structure data | 7bw7MC 7bw8C 7bwaC 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_30229.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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_30229_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_30229_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: HEK293T |
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: 1 / 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 | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Number grids imaged: 5 / #0 - Number real images: 17122 / #0 - Average exposure time: 10.0 sec. / #0 - Average electron dose: 50.0 e/Å2 #0 - Details: Images were collected in movie mode with 40 frames per 10 seconds. #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #1 - Detector mode: SUPER-RESOLUTION / #1 - Average electron dose: 50.0 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #2 - Detector mode: SUPER-RESOLUTION / #2 - Average electron dose: 50.0 e/Å2 |
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: 75 / Target criteria: Correlation coefficient | ||||||||
Output model | PDB-7bw7: |
-Atomic model buiding 2
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 90 / Target criteria: Correlation coefficient | ||||||||
Output model | PDB-7bw7: |