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- EMDB-36439: Cryo-EM structure of dengue virus serotype 3 strain 863DK in comp... -
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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 863DK in complex with human antibody DENV-290 Fab at 4 deg C | |||||||||
![]() | postprocessed map | |||||||||
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![]() | dengue virus / human antibody / dengue-antibody structure / virus | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | 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 | ![]() | 476.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20 KB 20 KB | Display Display | ![]() |
Images | ![]() | 246.7 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 404.2 MB 404.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1010.9 KB | Display | ![]() |
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Full document | ![]() | 1010.4 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | postprocessed map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.71 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_36439_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_36439_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Dengue virus serotype 3 strain 863DK in complex with human antibo...
Entire | Name: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-290 Fab at 4 deg C |
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Components |
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-Supramolecule #1: Dengue virus serotype 3 strain 863DK in complex with human antibo...
Supramolecule | Name: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-290 Fab at 4 deg C type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Dengue virus serotype 3 strain 863DK
Supramolecule | Name: Dengue virus serotype 3 strain 863DK / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: Human antibody DENV-290 Fab (heavy and light chain)
Supramolecule | Name: Human antibody DENV-290 Fab (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
Macromolecule | Name: Envelope protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | 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 |
-Macromolecule #2: Membrane protein
Macromolecule | Name: Membrane protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: SVALAPHVGM GLDTRTQTWM SAEGAWRQVE KVETWALRHP GFTILALFLA HYIGTSLTQK VVIFILLMLV TPSMT |
-Macromolecule #3: Human antibody DENV-290 heavy chain
Macromolecule | Name: Human antibody DENV-290 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: QVELVESGGD VVQPGKSLRL SCAASGFTFT NYAMHWLRQA PGKGLEWVAV ISSDVNDKYY ADSVKGRFTI SRDNSKNTLY LQMNSLTPE DTAVYYCARE QAVGTNPWAF DYWGQGTLVT VSS |
-Macromolecule #4: Human antibody DENV-290 light chain
Macromolecule | Name: Human antibody DENV-290 light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: HIVMTQSPLS LSVTPGQPAS ISCKSSQISS WGSDGKTYLY WYLQKPGQSP QLLIYEVSSR FSGVSDRFSG SGSGTDFTLK ISRVQAEDV GLYYCMQGLH LPLTFGQGTR LEIK |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
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-290 Fab 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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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm |
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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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 154214 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |