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- EMDB-36429: Cryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 ... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C (subparticle LLR-LRR) | |||||||||
![]() | postprocessed map | |||||||||
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Function / homology | ![]() clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Fibriansah G / Ng TS / Tan AWK / Shi J / Lok SM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Ultrapotent human antibodies lock E protein dimers of diverse DENV3 morphological variants Authors: Fibriansah G / Ng TS / Lim XN / Shebanova A / Ng LC / Tan SL / Tan AWK / Shi J / Crowe JE / Lok SM | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 31.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.2 KB 22.2 KB | Display Display | ![]() |
Images | ![]() | 240.5 KB | ||
Masks | ![]() | 34.3 MB | ![]() | |
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 24.9 MB 25 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jn1MC ![]() 8jn2C ![]() 8jn3C ![]() 8jn4C ![]() 8jn5C ![]() 8jn6C ![]() 8jn7C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | postprocessed map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.622 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_36429_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
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Density Histograms |
-Half map: half map 2
File | emd_36429_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Dengue virus serotype 3 strain EHIE46200Y19 in complex with human...
Entire | Name: Dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C |
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Components |
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-Supramolecule #1: Dengue virus serotype 3 strain EHIE46200Y19 in complex with human...
Supramolecule | Name: Dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Dengue virus serotype 3 strain EHIE46200Y19
Supramolecule | Name: Dengue virus serotype 3 strain EHIE46200Y19 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Supramolecule #3: Human antibody DENV-115 IgG (heavy and light chain)
Supramolecule | Name: Human antibody DENV-115 IgG (heavy and light chain) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Envelope protein (Fragment)
Macromolecule | Name: Envelope protein (Fragment) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 53.731734 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNVTT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLELIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST ...String: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNVTT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLELIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST VEAILPEYGT LGLECSPRTG LDFNEMILLT MKNKAWMVHR QWFFDLPLPW TSGATTETPT WNKKELLVTF KN AHAKKQE VVVLGSQEGA MHTALTGATE IQTSGGTSIF AGHLKCRLKM DKLELKGMSY AMCSNAFVLK KEVSETQHGT ILI KVEYKG EDAPCKIPFS TEDGQGKAHN GRLITANPVV TKKEELVNIE AEPPFGESNI IIGIGDKALR INWYKKGSSI GKMF EATAR GARRMAILGD TAWDFGSVGG VLNSLGKMVH QIFGSAYTAL FSGVSWIMKI GIGVLLTWIG LNSKNTSMSF SCIVI GIIT LYLGAVVQA UniProtKB: Genome polyprotein |
-Macromolecule #2: Polyprotein
Macromolecule | Name: Polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 8.365854 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: SVALAPHVGM GLDTRAQTWM SAEGAWRQIE KVETWAFRHP GFTILALFLA HYIGTSLTQK VVIFILLMLV TPSMT UniProtKB: Genome polyprotein |
-Macromolecule #3: Human antibody DENV-115 heavy chain
Macromolecule | Name: Human antibody DENV-115 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 13.607289 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QVQLVQSGAE VKKPGAPVKV SCEASGYTFT DYFIHWVRQA PGQGLEWMGW INPISGGTNY HPRFHGGVTM TRDTSMKVAY MELKRLTSD DTAVYFCARG RDFRGGYSQL DYWGQGTLVT VSS |
-Macromolecule #4: Human antibody DENV-115 light chain
Macromolecule | Name: Human antibody DENV-115 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.49662 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QSVLTQPPSA SGTPGQRVTI SCSGGSSNIA INTVNWYQQV PGTAPKLLMY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC ATWDDSLKDV LFGGGTKLTV L |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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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 mixed with DENV-115 IgG at a molar ratio of 1.5 Fab for every E-protein and then the mixture was incubated at 4 deg C for 30 min. |
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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: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 22.8 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic![]() |
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT | ||||||||
Output model | ![]() PDB-8jn1: |