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- EMDB-9651: Cryo-EM structure of Immature Dengue virus serotype 3 in complex ... -
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Open data
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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) | |||||||||||||||
![]() | Cryo-EM structure of immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 5.0 (Class II particle) | |||||||||||||||
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![]() | immature dengue virus / ![]() ![]() | |||||||||||||||
Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Wirawan M / Fibriansah G | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 220.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21.3 KB | Display | ![]() |
Images | ![]() | 156.8 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6idlMC ![]() 9649C ![]() 9650C ![]() 6idiC ![]() 6idkC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 53.682484 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 18.686615 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 15.319042 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 12.132362 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QSVLTQPPSA SGTPGQRVTI SCSGGSSNIG SSYVYWYKQV PGTAPKLLIY RNNERPSGVP DRFSGSKSGT SASLAISGLR SEDEADYYC AAWDDSLRGQ VFGGGTKLTV LGQPKAA |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD![]() |
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 |