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Yorodumi- EMDB-37425: CryoEM structure of non-structural protein 1 tetramer from Japane... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37425 | |||||||||
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Title | CryoEM structure of non-structural protein 1 tetramer from Japanese encephalitis virus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | flavivirus / non-structural protein 1 / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane ...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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / serine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Japanese encephalitis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Jiao HZ / Pan Q / Hu HL | |||||||||
Funding support | 1 items
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Citation | Journal: Sci Adv / Year: 2024 Title: The step-by-step assembly mechanism of secreted flavivirus NS1 tetramer and hexamer captured at atomic resolution. Authors: Qi Pan / Haizhan Jiao / Wanqin Zhang / Qiang Chen / Geshu Zhang / Jianhai Yu / Wei Zhao / Hongli Hu / Abstract: Flaviviruses encode a conserved, membrane-associated nonstructural protein 1 (NS1) with replication and immune evasion functions. The current knowledge of secreted NS1 (sNS1) oligomers is based on ...Flaviviruses encode a conserved, membrane-associated nonstructural protein 1 (NS1) with replication and immune evasion functions. The current knowledge of secreted NS1 (sNS1) oligomers is based on several low-resolution structures, thus hindering the development of drugs and vaccines against flaviviruses. Here, we revealed that recombinant sNS1 from flaviviruses exists in a dynamic equilibrium of dimer-tetramer-hexamer states. Two DENV4 hexameric NS1 structures and several tetrameric NS1 structures from multiple flaviviruses were solved at atomic resolution by cryo-EM. The stacking of the tetrameric NS1 and hexameric NS1 is facilitated by the hydrophobic β-roll and connector domains. Additionally, a triacylglycerol molecule located within the central cavity may play a role in stabilizing the hexamer. Based on differentiated interactions between the dimeric NS1, two distinct hexamer models (head-to-head and side-to-side hexamer) and the step-by-step assembly mechanisms of NS1 dimer into hexamer were proposed. We believe that our study sheds light on the understanding of the NS1 oligomerization and contributes to NS1-based therapies. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37425.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-37425-v30.xml emd-37425.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37425_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_37425.png | 188.5 KB | ||
Filedesc metadata | emd-37425.cif.gz | 5.4 KB | ||
Others | emd_37425_additional_1.map.gz emd_37425_half_map_1.map.gz emd_37425_half_map_2.map.gz | 47.7 MB 116.2 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37425 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37425 | HTTPS FTP |
-Validation report
Summary document | emd_37425_validation.pdf.gz | 898.2 KB | Display | EMDB validaton report |
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Full document | emd_37425_full_validation.pdf.gz | 897.8 KB | Display | |
Data in XML | emd_37425_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_37425_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37425 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37425 | HTTPS FTP |
-Related structure data
Related structure data | 8wbhMC 8wbbC 8wbcC 8wbdC 8wbeC 8wbfC 8wbgC 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_37425.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_37425_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_37425_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37425_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Japanese encephalitis virus non-structural protein 1 tetramer
Entire | Name: Japanese encephalitis virus non-structural protein 1 tetramer |
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Components |
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-Supramolecule #1: Japanese encephalitis virus non-structural protein 1 tetramer
Supramolecule | Name: Japanese encephalitis virus non-structural protein 1 tetramer type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Japanese encephalitis virus |
-Macromolecule #1: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Japanese encephalitis virus |
Molecular weight | Theoretical: 40.895074 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DTGCAIDITR KEMRCGSGIF VHNDVEAWVD RYKYLPETPR SLAKIVHKAH KEGVCGVRSV TRLEHQMWEA VRDELNVLLK ENAVDLSVV VNKPVGRYRS APKRLSMTQE KFEMGWKAWG KSILFAPELA NSTFVVDGPE TKECPDEHRA WNSMQIEDFG F GITSTRVW ...String: DTGCAIDITR KEMRCGSGIF VHNDVEAWVD RYKYLPETPR SLAKIVHKAH KEGVCGVRSV TRLEHQMWEA VRDELNVLLK ENAVDLSVV VNKPVGRYRS APKRLSMTQE KFEMGWKAWG KSILFAPELA NSTFVVDGPE TKECPDEHRA WNSMQIEDFG F GITSTRVW LKIREESTDE CDGAIIGTAV KGHVAVHSDL SYWIESRYND TWKLERAVFG EVKSCTWPET HTLWGDGVEE SE LIIPHTI AGPKSKHNRR EGYKTQNQGP WDENGIVLDF DYCPGTKVTI TEDCGKRGPS VRTTTDSGKL ITDWCCRSCS LPP LRFRTE NGCWYGMEIR PVRHDETTLV RSQVDAHHHH HH UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |