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Yorodumi- EMDB-36436: Cryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36436 | |||||||||
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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 | |||||||||
Map data | postprocessed map | |||||||||
Sample |
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Keywords | dengue virus / human antibody / dengue-antibody structure / virus | |||||||||
Biological species | Dengue virus type 3 / Homo sapiens (human) / dengue virus type 3 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Fibriansah G / Ng TS / Tan AWK / Shi J / Lok SM | |||||||||
Funding support | Singapore, 1 items
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Citation | Journal: To Be Published 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 | emd_36436.map.gz | 459.4 MB | EMDB map data format | |
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Header (meta data) | emd-36436-v30.xml emd-36436.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
Images | emd_36436.png | 263.2 KB | ||
Masks | emd_36436_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-36436.cif.gz | 5.6 KB | ||
Others | emd_36436_half_map_1.map.gz emd_36436_half_map_2.map.gz | 398.4 MB 398.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36436 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36436 | HTTPS FTP |
-Validation report
Summary document | emd_36436_validation.pdf.gz | 980.4 KB | Display | EMDB validaton report |
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Full document | emd_36436_full_validation.pdf.gz | 980 KB | Display | |
Data in XML | emd_36436_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_36436_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36436 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36436 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36436.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | postprocessed map | ||||||||||||||||||||
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
File | emd_36436_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_36436_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_36436_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-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: Dengue virus type 3 |
-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: Homo sapiens (human) |
-Macromolecule #1: Envelope protein
Macromolecule | Name: Envelope protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: dengue virus type 3 |
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 |
-Macromolecule #2: Membrane protein
Macromolecule | Name: Membrane protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: dengue virus type 3 |
Sequence | String: SVALAPHVGM GLDTRAQTWM SAEGAWRQIE KVETWAFRHP GFTILALFLA HYIGTSLTQK VVIFILLMLV TPSMT |
-Macromolecule #3: Human antibody DENV-115 heavy chain
Macromolecule | Name: Human antibody DENV-115 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
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 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QSVLTQPPSA SGTPGQRVTI SCSGGSSNIA INTVNWYQQV PGTAPKLLMY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC ATWDDSLKDV LFGGGTKLTV L |
-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 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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 22.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.6000000000000005 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 70158 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |