+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37678 | |||||||||
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Title | ZIKV rsNS1 in complex with Fab EB9 and anti-fab nanobody | |||||||||
Map data | ||||||||||
Sample |
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Keywords | antibody / flavivirus / zika / cryoEM / non structural protein 1 / ns1 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / 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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / 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 perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / GTP binding / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Zika virus / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 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_37678.map.gz | 777.6 MB | EMDB map data format | |
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Header (meta data) | emd-37678-v30.xml emd-37678.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37678_fsc.xml | 19.9 KB | Display | FSC data file |
Images | emd_37678.png | 170.8 KB | ||
Filedesc metadata | emd-37678.cif.gz | 6.2 KB | ||
Others | emd_37678_half_map_1.map.gz emd_37678_half_map_2.map.gz | 765.4 MB 765.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37678 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37678 | HTTPS FTP |
-Validation report
Summary document | emd_37678_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_37678_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_37678_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | emd_37678_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37678 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37678 | HTTPS FTP |
-Related structure data
Related structure data | 8wo4MC 8wn8C 8wnpC 8wnuC 8wo0C 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_37678.map.gz / Format: CCP4 / Size: 824 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: 0.68 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37678_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37678_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ZIKV rsNS1 in complex with Fab AA12 and anti-fab nanobody
Entire | Name: ZIKV rsNS1 in complex with Fab AA12 and anti-fab nanobody |
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Components |
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-Supramolecule #1: ZIKV rsNS1 in complex with Fab AA12 and anti-fab nanobody
Supramolecule | Name: ZIKV rsNS1 in complex with Fab AA12 and anti-fab nanobody type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: VL
Macromolecule | Name: VL / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.505992 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SDIQMTQSPF SLSASVGDRV TITCRASQSI SSHLNWYQQK PGKAPKFLIY AASSLQSGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYC QQSYSTPYTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: SDIQMTQSPF SLSASVGDRV TITCRASQSI SSHLNWYQQK PGKAPKFLIY AASSLQSGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYC QQSYSTPYTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #2: VH
Macromolecule | Name: VH / 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: 24.059949 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SEVQLVESGG GLIQPGGSLR LSCAASGFTV SSNYMSWVRQ APGKGLEWVS VIYSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARW GGKRGGAFDI WGQGTMVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String: SEVQLVESGG GLIQPGGSLR LSCAASGFTV SSNYMSWVRQ APGKGLEWVS VIYSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARW GGKRGGAFDI WGQGTMVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTHT |
-Macromolecule #3: Non-structural protein 1
Macromolecule | Name: Non-structural protein 1 / type: protein_or_peptide / ID: 3 / Details: NS1 / Number of copies: 2 / 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 #4: Anti-fab nanobody
Macromolecule | Name: Anti-fab nanobody / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 15.071431 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: HHHHHHGENL YFQGSQVQLQ ESGGGLVQPG GSLRLSCAAS GRTISRYAMS WFRQAPGKER EFVAVARRSG DGAFYADSVQ GRFTVSRDD AKNTVYLQMN SLKPEDTAVY YCAIDSDTFY SGSYDYWGQG TQVTVSS |
-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: 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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-8wo4: |