+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41138 | |||||||||
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Title | CryoEM structure of MFRV-VILP bound to IGF1Rzip | |||||||||
Map data | Map of MFRV-VILP bound to IGFRzip, reconstructed using 3D flexible refinement | |||||||||
Sample |
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Keywords | IGF1R / MFRV-VILP / VILP / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information cardiac atrium development / negative regulation of cholangiocyte apoptotic process / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / IRS-related events triggered by IGF1R / protein transporter activity / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / IRS-related events triggered by IGF1R / protein transporter activity / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to aldosterone / cellular response to zinc ion starvation / insulin receptor complex / insulin-like growth factor I binding / cellular response to testosterone stimulus / negative regulation of hepatocyte apoptotic process / insulin receptor activity / transcytosis / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / cellular response to angiotensin / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / insulin binding / response to L-glutamate / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / positive regulation of cytokinesis / positive regulation of axon regeneration / positive regulation of osteoblast proliferation / amyloid-beta clearance / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / insulin receptor substrate binding / response to vitamin E / G-protein alpha-subunit binding / estrous cycle / negative regulation of MAPK cascade / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / insulin-like growth factor receptor binding / T-tubule / phosphatidylinositol 3-kinase/protein kinase B signal transduction / axonogenesis / cellular response to dexamethasone stimulus / cerebellum development / insulin-like growth factor receptor signaling pathway / cellular response to estradiol stimulus / hippocampus development / response to nicotine / cellular response to glucose stimulus / positive regulation of smooth muscle cell proliferation / insulin receptor binding / regulation of protein phosphorylation / receptor protein-tyrosine kinase / caveola / hormone activity / cellular response to mechanical stimulus / cellular response to amyloid-beta / cellular senescence / positive regulation of cold-induced thermogenesis / insulin receptor signaling pathway / protein tyrosine kinase activity / response to ethanol / protein autophosphorylation / cell population proliferation / positive regulation of MAPK cascade / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / immune response / axon / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of apoptotic process / signal transduction / extracellular space / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Mandarin fish ranavirus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Kirk NS | |||||||||
Funding support | Czech Republic, 2 items
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Citation | Journal: Mol Metab / Year: 2024 Title: A viral insulin-like peptide inhibits IGF-1 receptor phosphorylation and regulates IGF1R gene expression. Authors: Martina Chrudinová / Nicholas S Kirk / Aurelien Chuard / Hari Venugopal / Fa Zhang / Marta Lubos / Vasily Gelfanov / Terezie Páníková / Lenka Žáková / Julianne Cutone / Matthew ...Authors: Martina Chrudinová / Nicholas S Kirk / Aurelien Chuard / Hari Venugopal / Fa Zhang / Marta Lubos / Vasily Gelfanov / Terezie Páníková / Lenka Žáková / Julianne Cutone / Matthew Mojares / Richard DiMarchi / Jiří Jiráček / Emrah Altindis / Abstract: OBJECTIVE: The insulin/IGF superfamily is conserved across vertebrates and invertebrates. Our team has identified five viruses containing genes encoding viral insulin/IGF-1 like peptides (VILPs) ...OBJECTIVE: The insulin/IGF superfamily is conserved across vertebrates and invertebrates. Our team has identified five viruses containing genes encoding viral insulin/IGF-1 like peptides (VILPs) closely resembling human insulin and IGF-1. This study aims to characterize the impact of Mandarin fish ranavirus (MFRV) and Lymphocystis disease virus-Sa (LCDV-Sa) VILPs on the insulin/IGF system for the first time. METHODS: We chemically synthesized single chain (sc, IGF-1 like) and double chain (dc, insulin like) forms of MFRV and LCDV-Sa VILPs. Using cell lines overexpressing either human insulin receptor ...METHODS: We chemically synthesized single chain (sc, IGF-1 like) and double chain (dc, insulin like) forms of MFRV and LCDV-Sa VILPs. Using cell lines overexpressing either human insulin receptor isoform A (IR-A), isoform B (IR-B) or IGF-1 receptor (IGF1R), and AML12 murine hepatocytes, we characterized receptor binding, insulin/IGF signaling. We further characterized the VILPs' effects of proliferation and IGF1R and IR gene expression, and compared them to native ligands. Additionally, we performed insulin tolerance test in CB57BL/6 J mice to examine in vivo effects of VILPs on blood glucose levels. Finally, we employed cryo-electron microscopy (cryoEM) to analyze the structure of scMFRV-VILP in complex with the IGF1R ectodomain. RESULTS: VILPs can bind to human IR and IGF1R, stimulate receptor autophosphorylation and downstream signaling pathways. Notably, scMFRV-VILP exhibited a particularly strong affinity for IGF1R, with ...RESULTS: VILPs can bind to human IR and IGF1R, stimulate receptor autophosphorylation and downstream signaling pathways. Notably, scMFRV-VILP exhibited a particularly strong affinity for IGF1R, with a mere 10-fold decrease compared to human IGF-1. At high concentrations, scMFRV-VILP selectively reduced IGF-1 stimulated IGF1R autophosphorylation and Erk phosphorylation (Ras/MAPK pathway), while leaving Akt phosphorylation (PI3K/Akt pathway) unaffected, indicating a potential biased inhibitory function. Prolonged exposure to MFRV-VILP led to a significant decrease in IGF1R gene expression in IGF1R overexpressing cells and AML12 hepatocytes. Furthermore, insulin tolerance test revealed scMFRV-VILP's sustained glucose-lowering effect compared to insulin and IGF-1. Finally, cryo-EM analysis revealed that scMFRV-VILP engages with IGF1R in a manner closely resembling IGF-1 binding, resulting in a highly analogous structure. CONCLUSIONS: This study introduces MFRV and LCDV-Sa VILPs as novel members of the insulin/IGF superfamily. Particularly, scMFRV-VILP exhibits a biased inhibitory effect on IGF1R signaling at high ...CONCLUSIONS: This study introduces MFRV and LCDV-Sa VILPs as novel members of the insulin/IGF superfamily. Particularly, scMFRV-VILP exhibits a biased inhibitory effect on IGF1R signaling at high concentrations, selectively inhibiting IGF-1 stimulated IGF1R autophosphorylation and Erk phosphorylation, without affecting Akt phosphorylation. In addition, MFRV-VILP specifically regulates IGF-1R gene expression and IGF1R protein levels without affecting IR. CryoEM analysis confirms that scMFRV-VILP' binding to IGF1R is mirroring the interaction pattern observed with IGF-1. These findings offer valuable insights into IGF1R action and inhibition, suggesting potential applications in development of IGF1R specific inhibitors and advancing long-lasting insulins. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41138.map.gz | 25.3 MB | EMDB map data format | |
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Header (meta data) | emd-41138-v30.xml emd-41138.xml | 21.3 KB 21.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41138_fsc.xml | 6.4 KB | Display | FSC data file |
Images | emd_41138.png | 73.4 KB | ||
Masks | emd_41138_msk_1.map | 3.4 MB | Mask map | |
Filedesc metadata | emd-41138.cif.gz | 7 KB | ||
Others | emd_41138_additional_1.map.gz emd_41138_half_map_1.map.gz emd_41138_half_map_2.map.gz | 1.7 MB 2 MB 2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41138 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41138 | HTTPS FTP |
-Validation report
Summary document | emd_41138_validation.pdf.gz | 601.8 KB | Display | EMDB validaton report |
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Full document | emd_41138_full_validation.pdf.gz | 601.4 KB | Display | |
Data in XML | emd_41138_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_41138_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41138 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41138 | HTTPS FTP |
-Related structure data
Related structure data | 8tanMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41138.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Map of MFRV-VILP bound to IGFRzip, reconstructed using 3D flexible refinement | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41138_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: DeepEMHancer-sharpened map of MFRV-VILP bound to IGFRzip, reconstructed...
File | emd_41138_additional_1.map | ||||||||||||
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Annotation | DeepEMHancer-sharpened map of MFRV-VILP bound to IGFRzip, reconstructed using 3D flexible refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map B of MFRV-VILP bound to IGFRzip, reconstructed...
File | emd_41138_half_map_1.map | ||||||||||||
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Annotation | Half-map B of MFRV-VILP bound to IGFRzip, reconstructed using 3D flexible refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map A of MFRV-VILP bound to IGFRzip, reconstructed...
File | emd_41138_half_map_2.map | ||||||||||||
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Annotation | Half-map A of MFRV-VILP bound to IGFRzip, reconstructed using 3D flexible refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 1:2 complex of MFRV-VILP bound to IGF1Rzip
Entire | Name: 1:2 complex of MFRV-VILP bound to IGF1Rzip |
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Components |
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-Supramolecule #1: 1:2 complex of MFRV-VILP bound to IGF1Rzip
Supramolecule | Name: 1:2 complex of MFRV-VILP bound to IGF1Rzip / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: MFRV-VILP
Supramolecule | Name: MFRV-VILP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Mandarin fish ranavirus / Synthetically produced: Yes |
-Supramolecule #3: IGF1Rzip
Supramolecule | Name: IGF1Rzip / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 Details: IGF1R ectodomain with C-terminal leucine zipper domain |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Insulin-like growth factor 1 receptor
Macromolecule | Name: Insulin-like growth factor 1 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: 108.937242 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLTV ITEYLLLFRV AGLESLGDLF PNLTVIRGWK LFYNYALVI FEMTNLKDIG LYNLRNITRG AIRIEKNADL CYLSTVDWSL ILDAVSNNYI VGNKPPKECG DLCPGTMEEK P MCEKTTIN ...String: EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLTV ITEYLLLFRV AGLESLGDLF PNLTVIRGWK LFYNYALVI FEMTNLKDIG LYNLRNITRG AIRIEKNADL CYLSTVDWSL ILDAVSNNYI VGNKPPKECG DLCPGTMEEK P MCEKTTIN NEYNYRCWTT NRCQKMCPST CGKRACTENN ECCHPECLGS CSAPDNDTAC VACRHYYYAG VCVPACPPNT YR FEGWRCV DRDFCANILS AESSDSEGFV IHDGECMQEC PSGFIRNGSQ SMYCIPCEGP CPKVCEEEKK TKTIDSVTSA QML QGCTIF KGNLLINIRR GNNIASELEN FMGLIEVVTG YVKIRHSHAL VSLSFLKNLR LILGEEQLEG NYSFYVLDNQ NLQQ LWDWD HRNLTIKAGK MYFAFNPKLC VSEIYRMEEV TGTKGRQSKG DINTRNNGER ASCESDVLHF TSTTTSKNRI IITWH RYRP PDYRDLISFT VYYKEAPFKN VTEYDGQDAC GSNSWNMVDV DLPPNKDVEP GILLHGLKPW TQYAVYVKAV TLTMVE NDH IRGAKSEILY IRTNASVPSI PLDVLSASNS SSQLIVKWNP PSLPNGNLSY YIVRWQRQPQ DGYLYRHNYC SKDKIPI RK YADGTIDIEE VTENPKTEVC GGEKGPCCAC PKTEAEKQAE KEEAEYRKVF ENFLHNSIFV PRPERKRRDV MQVANTTM S SRSRNTTAAD TYNITDPEEL ETEYPFFESR VDNKERTVIS NLRPFTLYRI DIHSCNHEAE KLGCSASNFV FARTMPAEG ADDIPGPVTW EPRPENSIFL KWPEPENPNG LILMYEIKYG SQVEDQRECV SRQEYRKYGG AKLNRLNPGN YTARIQATSL SGNGSWTDP VFFYVQAKTG YENFIHRMKQ LEDKVEELLS KNYHLENEVA RLKKLVGERS SSEQKLISEE DLN UniProtKB: Insulin-like growth factor 1 receptor |
-Macromolecule #2: Insulin-like growth factor
Macromolecule | Name: Insulin-like growth factor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mandarin fish ranavirus |
Molecular weight | Theoretical: 6.799011 KDa |
Sequence | String: VLTDKLCGKD LVDALLLVCG EKGVYSPKMG YARAKTVKGN GIADVCCTSA NGCDLNFLEK FCKT UniProtKB: Insulin-like growth factor |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 11 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.2 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00039000000000000005 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7833 / Average exposure time: 5.36 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 17.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |