+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8508 | |||||||||
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Title | Cryo-EM Structure of Immature Zika Virus | |||||||||
Map data | Cryo-EM Reconstruction of Immature Zika Virus | |||||||||
Sample |
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Function / homology | Function and homology information : / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / viral capsid ...: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 4 iron, 4 sulfur cluster binding / 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 / host cell surface / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / molecular adaptor activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / 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 / centrosome / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / GTP binding / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Zika virus / ZIKV (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.1 Å | |||||||||
Authors | Mangala Prasad V / Miller AS / Klose T / Sirohi D / Buda G / Jiang W / Kuhn RJ / Rossmann MG | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2017 Title: Structure of the immature Zika virus at 9 Å resolution. Authors: Vidya Mangala Prasad / Andrew S Miller / Thomas Klose / Devika Sirohi / Geeta Buda / Wen Jiang / Richard J Kuhn / Michael G Rossmann / Abstract: The current Zika virus (ZIKV) epidemic is characterized by severe pathogenicity in both children and adults. Sequence changes in ZIKV since its first isolation are apparent when pre-epidemic strains ...The current Zika virus (ZIKV) epidemic is characterized by severe pathogenicity in both children and adults. Sequence changes in ZIKV since its first isolation are apparent when pre-epidemic strains are compared with those causing the current epidemic. However, the residues that are responsible for ZIKV pathogenicity are largely unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of the immature ZIKV at 9-Å resolution. The cryo-EM map was fitted with the crystal structures of the precursor membrane and envelope glycoproteins and was shown to be similar to the structures of other known immature flaviviruses. However, the immature ZIKV contains a partially ordered capsid protein shell that is less prominent in other immature flaviviruses. Furthermore, six amino acids near the interface between pr domains at the top of the spikes were found to be different between the pre-epidemic and epidemic ZIKV, possibly influencing the composition and structure of the resulting viruses. | |||||||||
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_8508.map.gz | 56.3 MB | EMDB map data format | |
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Header (meta data) | emd-8508-v30.xml emd-8508.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8508_fsc.xml | 14 KB | Display | FSC data file |
Images | emd_8508.png | 289.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8508 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8508 | HTTPS FTP |
-Related structure data
Related structure data | 5u4wMC M: atomic model generated by this map C: citing same article (ref.) |
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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_8508.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM Reconstruction of Immature Zika Virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-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-#4 / NCBI-ID: 64320 / Sci species name: Zika virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Name: prM-E glycoprotein / Diameter: 600.0 Å / T number (triangulation number): 1 |
-Supramolecule #2: Transmembrane domains
Supramolecule | Name: Transmembrane domains / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Zika virus |
-Macromolecule #1: E protein
Macromolecule | Name: E protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Zika virus |
Molecular weight | Theoretical: 44.80141 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: GENLYFQGMR CIGMSNRDFV EGVSGGSWVD IVLEHGSCVT TMAKNKPTLD FELIKTEAKQ PATLRKYCIE AKLTNTTTES RCPTQGEPS LNEEQDKRFV CKHSMVDRGW GNGCGLFGKG GIVTCAMFRC KKNMEGKVVQ PENLEYTIVI TPHSGEEHAV G NDTGKHGK ...String: GENLYFQGMR CIGMSNRDFV EGVSGGSWVD IVLEHGSCVT TMAKNKPTLD FELIKTEAKQ PATLRKYCIE AKLTNTTTES RCPTQGEPS LNEEQDKRFV CKHSMVDRGW GNGCGLFGKG GIVTCAMFRC KKNMEGKVVQ PENLEYTIVI TPHSGEEHAV G NDTGKHGK EIKITPQSSI TEAELTGYGT VTMECSPRTG LDFNEMVLLQ MENKAWLVHR QWFLDLPLPW LPGADTQGSN WI QKETLVT FKNPHAKKQD VVVLGSQEGA MHTALTGATE IQMSSGNLLF TGHLKCRLRM DKLQLKGMSY SMCTGKFKVV KEI AETQHG TIVIRVQYEG DGSPCKIPFE IMDLEKRHVL GRLITVNPIV TEKDSPVNIE AEPPFGDSYI IIGVEPGQLK LNWF KK |
-Macromolecule #2: pr domain
Macromolecule | Name: pr domain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Zika virus |
Molecular weight | Theoretical: 9.261531 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: FHLTTRNGEP HMIVSRQEKG KSLLFKTEDG VNMCTLMAMD LGELCEDTIT YKCPLLRQNE PEDIDCWCNS TSTWVTYGTC T |
-Macromolecule #3: Protein E
Macromolecule | Name: Protein E / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ZIKV (virus) |
Molecular weight | Theoretical: 6.892228 KDa |
Sequence | String: GALNSLGKGI HQIFGAAFKS LFGGMSWFSQ ILIGTLLMWL GLNTKNGSIS LMCLALGGVL IFLSTA |
-Macromolecule #4: M protein
Macromolecule | Name: M protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ZIKV (virus) |
Molecular weight | Theoretical: 5.984065 KDa |
Sequence | String: REYTKHLIRV ENWIFRNPGF ALAAAAIAWL LGSSTSQKVI YLVMILLIAP AYS |
-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: 12 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #6: beta-D-mannopyranose
Macromolecule | Name: beta-D-mannopyranose / type: ligand / ID: 6 / Number of copies: 6 / Formula: BMA |
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Molecular weight | Theoretical: 180.156 Da |
Chemical component information | ChemComp-BMA: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Ultrathin carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Instrument: GATAN CRYOPLUNGE 3 |
-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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 3341 / Average exposure time: 7.6 sec. / Average electron dose: 4.7 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
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Output model | PDB-5u4w: |