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Yorodumi- PDB-7c2s: Helical reconstruction of Dengue virus serotype 3 complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c2s | |||||||||
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Title | Helical reconstruction of Dengue virus serotype 3 complexed with Fab C10 | |||||||||
Components |
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Keywords | VIRUS / antibody / neutralization | |||||||||
Function / homology | Function and homology information flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Dengue virus 3 | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10.4 Å | |||||||||
Authors | Morrone, S. / Chew, S.V. / Lim, X.N. / Ng, T.S. / Kostyuchenko, V.A. / Zhang, S. / Lok, S.M. | |||||||||
Funding support | Singapore, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: High flavivirus structural plasticity demonstrated by a non-spherical morphological variant. Authors: Seamus R Morrone / Valerie S Y Chew / Xin-Ni Lim / Thiam-Seng Ng / Victor A Kostyuchenko / Shuijun Zhang / Melissa Wirawan / Pau-Ling Chew / Jaime Lee / Joanne L Tan / Jiaqi Wang / Ter Yong ...Authors: Seamus R Morrone / Valerie S Y Chew / Xin-Ni Lim / Thiam-Seng Ng / Victor A Kostyuchenko / Shuijun Zhang / Melissa Wirawan / Pau-Ling Chew / Jaime Lee / Joanne L Tan / Jiaqi Wang / Ter Yong Tan / Jian Shi / Gavin Screaton / Marc C Morais / Shee-Mei Lok / Abstract: Previous flavivirus (dengue and Zika viruses) studies showed largely spherical particles either with smooth or bumpy surfaces. Here, we demonstrate flavivirus particles have high structural ...Previous flavivirus (dengue and Zika viruses) studies showed largely spherical particles either with smooth or bumpy surfaces. Here, we demonstrate flavivirus particles have high structural plasticity by the induction of a non-spherical morphology at elevated temperatures: the club-shaped particle (clubSP), which contains a cylindrical tail and a disc-like head. Complex formation of DENV and ZIKV with Fab C10 stabilize the viruses allowing cryoEM structural determination to ~10 Å resolution. The caterpillar-shaped (catSP) Fab C10:ZIKV complex shows Fabs locking the E protein raft structure containing three E dimers. However, compared to the original spherical structure, the rafts have rotated relative to each other. The helical tail structure of Fab C10:DENV3 clubSP showed although the Fab locked an E protein dimer, the dimers have shifted laterally. Morphological diversity, including clubSP and the previously identified bumpy and smooth-surfaced spherical particles, may help flavivirus survival and immune evasion. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7c2s.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c2s.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 7c2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c2s_validation.pdf.gz | 817.3 KB | Display | wwPDB validaton report |
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Full document | 7c2s_full_validation.pdf.gz | 816.9 KB | Display | |
Data in XML | 7c2s_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 7c2s_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/7c2s ftp://data.pdbj.org/pub/pdb/validation_reports/c2/7c2s | HTTPS FTP |
-Related structure data
Related structure data | 30278MC 7c2tC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 43322.457 Da / Num. of mol.: 2 / Fragment: ectodomain / Source method: isolated from a natural source / Source: (natural) Dengue virus 3 / References: UniProt: Q07019, UniProt: O39791*PLUS #2: Antibody | Mass: 14487.058 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) #3: Antibody | Mass: 11298.362 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293-6E | ||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 18 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 102.3 ° / Axial rise/subunit: 18.5 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7051 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
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