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Yorodumi- EMDB-30278: Helical reconstruction of Dengue virus serotype 3 complexed with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30278 | |||||||||
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Title | Helical reconstruction of Dengue virus serotype 3 complexed with Fab C10 | |||||||||
Map data | helical reconstruction of DENV3 complexed with Fab C10 | |||||||||
Sample |
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Keywords | antibody / neutralization / VIRUS | |||||||||
Function / homology | Function and homology information flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Dengue virus 3 | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 10.4 Å | |||||||||
Authors | Morrone S / Chew SV | |||||||||
Funding support | Singapore, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30278.map.gz | 48.7 MB | EMDB map data format | |
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Header (meta data) | emd-30278-v30.xml emd-30278.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_30278.png | 85 KB | ||
Filedesc metadata | emd-30278.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30278 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30278 | HTTPS FTP |
-Related structure data
Related structure data | 7c2sMC 7c2tC 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_30278.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | helical reconstruction of DENV3 complexed with Fab C10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.71 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 : Helical reconstruction of Dengue virus serotype 3 complexed with ...
Entire | Name: Helical reconstruction of Dengue virus serotype 3 complexed with Fab C10 |
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Components |
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-Supramolecule #1: Helical reconstruction of Dengue virus serotype 3 complexed with ...
Supramolecule | Name: Helical reconstruction of Dengue virus serotype 3 complexed with Fab C10 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: C10 Fab
Supramolecule | Name: C10 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Dengue virus serotype 3
Supramolecule | Name: Dengue virus serotype 3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Dengue virus 3 |
-Macromolecule #1: envelope protein
Macromolecule | Name: envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Dengue virus 3 |
Molecular weight | Theoretical: 43.322457 KDa |
Sequence | String: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLESIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST ...String: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLESIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST VEAILPEYGT LGLECSPRTG LDFNEMILLT MKNKAWMVHR QWFFDLPLPW TSGATTETPT WNRKELLVTF KN AHAKKQE VVVLGSQEGA MHTALTGATE IQNSGGTSIF AGHLKCRLKM DKLELKGMSY AMCLNTFVLK KEVSETQHGT ILI KVEYKG EDAPCKIPFS TEDGQGKAHN GRLITANPVV TKKEEPVNIE AEPPFGESNI VIGIGDKALK INWYKKGS UniProtKB: Genome polyprotein |
-Macromolecule #2: Heavy chain of Fab C10
Macromolecule | Name: Heavy chain of Fab C10 / 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: 14.487058 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGAE VKKPGASVKV SCKASGYTFT SYAMHWVRQA PGQRLEWMGW INAGNGNTKY SQKFQDRVTI TRDTSASTAY MELSSLRSE DTAIYYCARD KVDDYGDYWF PTLWYFDYWG QGTLVTVS |
-Macromolecule #3: light chain of Fab C10
Macromolecule | Name: light chain of Fab C10 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.298362 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SALTQPASVS GSPGQSITIS CTGTSSDVGG FNYVSWFQQH PGKAPKLMLY DVTSRPSGVS SRFSGSKSGN TASLTISGLQ AEDEADYYC SSHTSRGTWV FGGGTKLTVL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 18.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 18.5 Å Applied symmetry - Helical parameters - Δ&Phi: 102.3 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7051 |