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Yorodumi- EMDB-9651: Cryo-EM structure of Immature Dengue virus serotype 3 in complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9651 | |||||||||||||||
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Title | Cryo-EM structure of Immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 5.0 (Class II particle) | |||||||||||||||
Map data | Cryo-EM structure of immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 5.0 (Class II particle) | |||||||||||||||
Sample |
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Keywords | immature dengue virus / human antibody / VIRUS | |||||||||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Dengue virus 3 | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 25.0 Å | |||||||||||||||
Authors | Wirawan M / Fibriansah G | |||||||||||||||
Funding support | Singapore, United States, 4 items
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Citation | Journal: Structure / Year: 2019 Title: Mechanism of Enhanced Immature Dengue Virus Attachment to Endosomal Membrane Induced by prM Antibody. Authors: Melissa Wirawan / Guntur Fibriansah / Jan K Marzinek / Xin Xiang Lim / Thiam-Seng Ng / Adelene Y L Sim / Qian Zhang / Victor A Kostyuchenko / Jian Shi / Scott A Smith / Chandra S Verma / ...Authors: Melissa Wirawan / Guntur Fibriansah / Jan K Marzinek / Xin Xiang Lim / Thiam-Seng Ng / Adelene Y L Sim / Qian Zhang / Victor A Kostyuchenko / Jian Shi / Scott A Smith / Chandra S Verma / Ganesh Anand / James E Crowe / Peter J Bond / Shee-Mei Lok / Abstract: Dengue virus (DENV) particles are released from cells in different maturation states. Fully immature DENV (immDENV) is generally non-infectious, but can become infectious when complexed with anti- ...Dengue virus (DENV) particles are released from cells in different maturation states. Fully immature DENV (immDENV) is generally non-infectious, but can become infectious when complexed with anti-precursor membrane (prM) protein antibodies. It is unknown how anti-prM antibody-coated particles can undergo membrane fusion since the prM caps the envelope (E) protein fusion loop. Here, we determined cryoelectron microscopy (cryo-EM) maps of the immDENV:anti-prM complex at different pH values, mimicking the extracellular (pH 8.0) or endosomal (pH 5.0) environments. At pH 5.0, there are two structural classes with fewer antibodies bound than at pH 8.0. These classes may represent different maturation states. Molecular simulations, together with the measured high-affinity pr:antibody interaction (versus the weak pr:E interaction) and also the low pH cryo-EM structures, suggest how antibody:pr complex can dislodge from the E protein at low pH. This exposes the E protein fusion loop enhancing virus interaction with endosomes. | |||||||||||||||
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_9651.map.gz | 220.8 MB | EMDB map data format | |
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Header (meta data) | emd-9651-v30.xml emd-9651.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9651_fsc.xml | 21.3 KB | Display | FSC data file |
Images | emd_9651.png | 156.8 KB | ||
Filedesc metadata | emd-9651.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9651 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9651 | HTTPS FTP |
-Validation report
Summary document | emd_9651_validation.pdf.gz | 454.6 KB | Display | EMDB validaton report |
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Full document | emd_9651_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | emd_9651_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_9651_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9651 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9651 | HTTPS FTP |
-Related structure data
Related structure data | 6idlMC 9649C 9650C 6idiC 6idkC C: citing same article (ref.) M: atomic model generated by this map |
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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_9651.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 5.0 (Class II particle) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.7 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 : Dengue virus 3 in complex with human antibodies
Entire | Name: Dengue virus 3 in complex with human antibodies |
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Components |
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-Supramolecule #1: Dengue virus 3 in complex with human antibodies
Supramolecule | Name: Dengue virus 3 in complex with human antibodies / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The virus was isolated from dengue patient. The immature dengue 3 virus was grown in Aedes Albopictus clone C6/36 cell. The anti-prM antibody 1H10 was generated from EBV-immortalized PBMC ...Details: The virus was isolated from dengue patient. The immature dengue 3 virus was grown in Aedes Albopictus clone C6/36 cell. The anti-prM antibody 1H10 was generated from EBV-immortalized PBMC that was obtained from dengue patient. |
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-Supramolecule #4: Fab of antibody 1H10
Supramolecule | Name: Fab of antibody 1H10 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: Dengue virus 3
Supramolecule | Name: Dengue virus 3 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1 / NCBI-ID: 11069 / Sci species name: Dengue virus 3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Supramolecule #3: Dengue virus 3
Supramolecule | Name: Dengue virus 3 / type: virus / ID: 3 / Parent: 1 / Macromolecule list: #2 / NCBI-ID: 11069 / Sci species name: Dengue virus 3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: Envelope protein
Macromolecule | Name: Envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Dengue virus 3 |
Molecular weight | Theoretical: 53.682484 KDa |
Recombinant expression | Organism: Aedes albopictus (Asian tiger mosquito) |
Sequence | String: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA VLPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLEPIEGKV VQYENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST ...String: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA VLPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLEPIEGKV VQYENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST TEAILPEYGT LGLECSPRTG LDFNEMILLT MKNKAWMVHR QWFFDLPLPW ASGATTETPT WNRKELLVTF KN AHAKKQE VVVLGSQEGA MHTALTGATE IQNSGGTSIF AGHLKCRLKM DKLELKGMSY AMCTNTFVLK KEVSETQHGT ILI KVEYKG EDAPCKIPFS TEDGQGKAHN GRLITANPVV TKKEEPVNIE AEPPFGESNI VIGIGDNALK INWYKKGSSI GKMF EATAR GARRMAILGD TAWDFGSVGG VLNSLGKMVH QIFGSAYTAL FSGVSWVMKI GIGVLLTWIG LNSKNTSMSF SCIAI GIIT LYLGAVVQA UniProtKB: Genome polyprotein |
-Macromolecule #2: Premembrane protein
Macromolecule | Name: Premembrane protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Dengue virus 3 |
Molecular weight | Theoretical: 18.686615 KDa |
Recombinant expression | Organism: Aedes albopictus (Asian tiger mosquito) |
Sequence | String: FHLTSRDGEP RMIVGKNERG KSLLFKTASG INMCTLIAMD LGEMCDDTVT YKCPHITEVE PEDIDCWCNL TSTWVTYGTC NQAGEHRRD KRSVALAPHV GMGLDTRTQT WMSAEGAWRQ VEKVETWALR HPGFTILALF LAHYIGTSLT QKVVIFILLM L VTPSMT UniProtKB: Genome polyprotein |
-Macromolecule #3: Fab 1H10 heavy chain (V-region)
Macromolecule | Name: Fab 1H10 heavy chain (V-region) / 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: 15.319042 KDa |
Recombinant expression | Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) |
Sequence | String: QVQLVESGGG VVQPGRSLRL SCAASGFTFS NFAMHWVRQA PGKGLEWVSL ISYDGSNKYN ADSVRGRFSI SRDNSKNTLY LQMNSLRLE DTAVYYCVRV RQPWTQAWST NYFYYYGMDV WGQGTTVTVS SASTKGPS |
-Macromolecule #4: Fab 1H10 light chain (V-region)
Macromolecule | Name: Fab 1H10 light chain (V-region) / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.132362 KDa |
Recombinant expression | Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) |
Sequence | String: QSVLTQPPSA SGTPGQRVTI SCSGGSSNIG SSYVYWYKQV PGTAPKLLIY RNNERPSGVP DRFSGSKSGT SASLAISGLR SEDEADYYC AAWDDSLRGQ VFGGGTKLTV LGQPKAA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 18.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 47000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |