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Yorodumi- EMDB-30883: Cryo-EM structure of Dengue virus serotype 1 strain WestPac 74 in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30883 | ||||||||||||
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Title | Cryo-EM structure of Dengue virus serotype 1 strain WestPac 74 in complex with human antibody 1C19 Fab at 37 deg C (Class 1 particle) | ||||||||||||
Map data | CryoEM map of DENV1 strain WestPac 74 in complex with Fab 1C19 at 37 deg C (Class 1) | ||||||||||||
Sample |
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Keywords | dengue virus / human antibody / dengue-Fab structure / VIRUS / VIRUS-IMMUNE SYSTEM complex | ||||||||||||
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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / 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 / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Dengue virus 1 / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 19.0 Å | ||||||||||||
Authors | Fibriansah G / Ng TS | ||||||||||||
Funding support | Singapore, United States, 3 items
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Citation | Journal: PLoS Pathog / Year: 2021 Title: Antibody affinity versus dengue morphology influences neutralization. Authors: Guntur Fibriansah / Elisa X Y Lim / Jan K Marzinek / Thiam-Seng Ng / Joanne L Tan / Roland G Huber / Xin-Ni Lim / Valerie S Y Chew / Victor A Kostyuchenko / Jian Shi / Ganesh S Anand / Peter ...Authors: Guntur Fibriansah / Elisa X Y Lim / Jan K Marzinek / Thiam-Seng Ng / Joanne L Tan / Roland G Huber / Xin-Ni Lim / Valerie S Y Chew / Victor A Kostyuchenko / Jian Shi / Ganesh S Anand / Peter J Bond / James E Crowe / Shee-Mei Lok / Abstract: Different strains within a dengue serotype (DENV1-4) can have smooth, or "bumpy" surface morphologies with different antigenic characteristics at average body temperature (37°C). We determined the ...Different strains within a dengue serotype (DENV1-4) can have smooth, or "bumpy" surface morphologies with different antigenic characteristics at average body temperature (37°C). We determined the neutralizing properties of a serotype cross-reactive human monoclonal antibody (HMAb) 1C19 for strains with differing morphologies within the DENV1 and DENV2 serotypes. We mapped the 1C19 epitope to E protein domain II by hydrogen deuterium exchange mass spectrometry, cryoEM and molecular dynamics simulations, revealing that this epitope is likely partially hidden on the virus surface. We showed the antibody has high affinity for binding to recombinant DENV1 E proteins compared to those of DENV2, consistent with its strong neutralizing activities for all DENV1 strains tested regardless of their morphologies. This finding suggests that the antibody could out-compete E-to-E interaction for binding to its epitope. In contrast, for DENV2, HMAb 1C19 can only neutralize when the epitope becomes exposed on the bumpy-surfaced particle. Although HMAb 1C19 is not a suitable therapeutic candidate, this study with HMAb 1C19 shows the importance of choosing a high-affinity antibody that could neutralize diverse dengue virus morphologies for therapeutic purposes. | ||||||||||||
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_30883.map.gz | 223.2 MB | EMDB map data format | |
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Header (meta data) | emd-30883-v30.xml emd-30883.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
Images | emd_30883.png | 184.3 KB | ||
Filedesc metadata | emd-30883.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30883 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30883 | HTTPS FTP |
-Related structure data
Related structure data | 7dwtMC 7dwuC 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_30883.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of DENV1 strain WestPac 74 in complex with Fab 1C19 at 37 deg C (Class 1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Dengue virus serotype 1 strain WestPac 74 in complex with human a...
Entire | Name: Dengue virus serotype 1 strain WestPac 74 in complex with human antibody 1C19 Fab |
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Components |
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-Supramolecule #1: Dengue virus serotype 1 strain WestPac 74 in complex with human a...
Supramolecule | Name: Dengue virus serotype 1 strain WestPac 74 in complex with human antibody 1C19 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Dengue virus serotype 1 strain WestPac 74 was grown in Aedes albopictus C6/36 cells. |
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Source (natural) | Organism: Dengue virus 1 / Strain: Western Pacific 74 |
-Supramolecule #2: Dengue virus 1
Supramolecule | Name: Dengue virus 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Dengue virus serotype 1 strain WestPac 74 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: antibody 1C19 Fab
Supramolecule | Name: antibody 1C19 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: antibody 1C19 Fab |
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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 1 / Strain: WestPac 74 |
Molecular weight | Theoretical: 53.910871 KDa |
Sequence | String: MRCVGIGNRD FVEGLSGATW VDVVLEHGSC VTTMAKDKPT LDIELLKTEV TNPAVLRKLC IEAKISNTTT DSRCPTQGEA TLVEEQDTN FVCRRTFVDR GWGNGCGLFG KGSLITCAKF KCVTKLEGKI VQYENLKYSV IVTVHTGDQH QVGNETTEHG T IATITPQA ...String: MRCVGIGNRD FVEGLSGATW VDVVLEHGSC VTTMAKDKPT LDIELLKTEV TNPAVLRKLC IEAKISNTTT DSRCPTQGEA TLVEEQDTN FVCRRTFVDR GWGNGCGLFG KGSLITCAKF KCVTKLEGKI VQYENLKYSV IVTVHTGDQH QVGNETTEHG T IATITPQA PTSEIQLTDY GALTLDCSPR TGLDFNEMVL LTMEKKSWLV HKQWFLDLPL PWTSGASTSQ ETWNRQDLLV TF KTAHAKK QEVVVLGSQE GAMHTALTGA TEIQTSGTTT IFAGHLKCRL KMDKLTLKGM SYVMCTGSFK LEKEVAETQH GTV LVQVKY EGTDAPCKIP FSSQDEKGVT QNGRLITANP IVTDKEKPVN IEAEPPFGES YIVVGAGEKA LKLSWFKKGS SIGK MFEAT ARGARRMAIL GDTAWDFGSI GGVFTSVGKL IHQIFGTAYG VLFSGVSWTM KIGIGILLTW LGLNSRSTSL SMTCI AVGM VTLYLGVMVQ A |
-Macromolecule #2: Anti-dengue virus human monoclonal antibody 1C19 Fab heavy chain
Macromolecule | Name: Anti-dengue virus human monoclonal antibody 1C19 Fab heavy chain type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.167631 KDa |
Sequence | String: QVQLVESGGG VVQPGRSLRL SCAASGFIFS NYGMHWVRQA PGKGLEWVAV ISYDGSDKRY ADSVRGRFTI SRDNSKNTLF LQVTSLRAE DTAVYYCAKE LSGYDPGFEY WGQGTPVTVS S |
-Macromolecule #3: Anti-dengue virus human monoclonal antibody 1C19 Fab light chain
Macromolecule | Name: Anti-dengue virus human monoclonal antibody 1C19 Fab light chain type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.584849 KDa |
Sequence | String: DIQMTQSPST LSASVGDRVT ITCRASQSIN TWLAWYQQKP GKAPKLLIYK ASSLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYESYATFGQ GTKVDIK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Details: NTE buffer (12 mM Tris-HCl pH 8.0, 120 mM NaCl and 1 mM EDTA) |
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Vitrification | Cryogen name: ETHANE |
Details | The purified virus was incubated with Fab 1C19 at 37 deg C for 30 min with a molar ratio of one Fab for every E-protein and followed by incubation at 4 deg C for 2 h. |
-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: FEI FALCON II (4k x 4k) / Average electron dose: 18.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 4301 |
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Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: COMMON LINE / Software - Name: MPSA |
Final angle assignment | Type: COMMON LINE / Software - Name: MPSA |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MPSA / Number images used: 1116 |
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: RIGID BODY FIT | ||||||||
Output model | PDB-7dwt: |