+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37663 | |||||||||
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Title | CryoEM structure of ZIKV rsNS1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Flavivirus / ZIKA / NS1 / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Zika virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Chew BLA / Luo D | |||||||||
Funding support | Singapore, 1 items
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Citation | Journal: Npj Viruses / Year: 2024 Title: Structural basis of Zika virus NS1 multimerization and human antibody recognition Authors: Chew BLA / Ngoh AQ / Phoo WW / Weng MJG / Sheng HJ / Chan KWK / Tan EYJ / Gelbart T / Xu C / Tan GS / Vasudevan SG / Luo D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37663.map.gz | 33 MB | EMDB map data format | |
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Header (meta data) | emd-37663-v30.xml emd-37663.xml | 14 KB 14 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37663_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_37663.png | 104.4 KB | ||
Filedesc metadata | emd-37663.cif.gz | 5.5 KB | ||
Others | emd_37663_half_map_1.map.gz emd_37663_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37663 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37663 | HTTPS FTP |
-Related structure data
Related structure data | 8wn8MC 8wnpC 8wnuC 8wo0C 8wo4C 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_37663.map.gz / Format: CCP4 / Size: 64 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: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37663_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37663_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Zika virus
Entire | Name: Zika virus |
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Components |
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-Supramolecule #1: Zika virus
Supramolecule | Name: Zika virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: NS1 / NCBI-ID: 64320 / Sci species name: Zika virus / Sci species strain: MR766 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Non-structural protein 1
Macromolecule | Name: Non-structural protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Zika virus |
Molecular weight | Theoretical: 41.251578 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DVGCSVDFSK KETRCGTGVF IYNDVEAWRD RYKYHPDSPR RLAAAVKQAW EEGICGISSV SRMENIMWKS VEGELNAILE ENGVQLTVV VGSVKNPMWR GPQRLPVPVN ELPHGWKAWG KSYFVRAAKT NNSFVVDGDT LKECPLEHRA WNSFLVEDHG F GVFHTSVW ...String: DVGCSVDFSK KETRCGTGVF IYNDVEAWRD RYKYHPDSPR RLAAAVKQAW EEGICGISSV SRMENIMWKS VEGELNAILE ENGVQLTVV VGSVKNPMWR GPQRLPVPVN ELPHGWKAWG KSYFVRAAKT NNSFVVDGDT LKECPLEHRA WNSFLVEDHG F GVFHTSVW LKVREDYSLE CDPAVIGTAV KGREAAHSDL GYWIESEKND TWRLKRAHLI EMKTCEWPKS HTLWTDGVEE SD LIIPKSL AGPLSHHNTR EGYRTQVKGP WHSEELEIRF EECPGTKVYV EETCGTRGPS LRSTTASGRV IEEWCCRECT MPP LSFRAK DGCWYGMEIR PRKEPESNLV RSMVTAGTKH HHHHH UniProtKB: Genome polyprotein |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 2 / 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
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8wn8: |