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Yorodumi- EMDB-36441: Cryo-EM structure of dengue virus serotype 3 strain CH53489 spher... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36441 | |||||||||
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Title | Cryo-EM structure of dengue virus serotype 3 strain CH53489 spherical particle in complex with human antibody DENV-290 Fab at 37 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) / Aedes albopictus (Asian tiger mosquito) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.6 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_36441.map.gz | 472.6 MB | EMDB map data format | |
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Header (meta data) | emd-36441-v30.xml emd-36441.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_36441.png | 232.5 KB | ||
Masks | emd_36441_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-36441.cif.gz | 5.9 KB | ||
Others | emd_36441_half_map_1.map.gz emd_36441_half_map_2.map.gz | 404.2 MB 404.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36441 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36441 | HTTPS FTP |
-Validation report
Summary document | emd_36441_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_36441_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_36441_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_36441_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36441 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36441 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36441.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | postprocessed map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
File | emd_36441_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_36441_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_36441_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 CH53489 in complex with human anti...
Entire | Name: Dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C |
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Components |
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-Supramolecule #1: Dengue virus serotype 3 strain CH53489 in complex with human anti...
Supramolecule | Name: Dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Dengue virus serotype 3 strain CH53489
Supramolecule | Name: Dengue virus serotype 3 strain CH53489 / 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-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: 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: Aedes albopictus (Asian tiger mosquito) |
Sequence | String: mrcvgvgnrd fveglsgat w vdvvlehg gc vttmakn kpt ldielq ktea tqlat lrklc iegk itnitt dsr cptqgea vl peeqdqny v ckhtyvdrg wgngcglfgk gslvtcakf q clepiegk vv qyenlky tvi itvhtg dqhq vgnet ...String: mrcvgvgnrd fveglsgat w vdvvlehg gc vttmakn kpt ldielq ktea tqlat lrklc iegk itnitt dsr cptqgea vl peeqdqny v ckhtyvdrg wgngcglfgk gslvtcakf q clepiegk vv qyenlky tvi itvhtg dqhq vgnet qgvta eitp qastte ail peygtlg le csprtgld f nemilltmk nkawmvhrqw ffdlplpwa s gattetpt wn rkellvt fkn ahakkq evvv lgsqe gamht altg ateiqn sgg tsifagh lk crlkmdkl e lkgmsyamc tntfvlkkev setqhgtil i kveykged ap ckipfst edg qgkahn grli tanpv vtkke epvn ieaepp fge snivigi gd nalkinwy k kgssigkmf eatargarrm ailgdtawd f gsvggvln sl gkmvhqi fgs aytalf sgvs wvmki gigvl ltwi glnskn tsm sfsciai gi itlylgav v qa |
-Macromolecule #2: Membrane protein
Macromolecule | Name: Membrane protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Aedes albopictus (Asian tiger mosquito) |
Sequence | String: svala phvg mgldtr tqt wmsaega wr qvekvetw a lrhpgftil alflahyigt sltqkvvif i llmlvtps mt |
-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: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVELVESGGD VVQPGKSLRL SCAASGFTFT NYAMHWLRQA PGKGLEWVAV ISSDVNDKYY ADSVKGRFTI SRDNSKNTLY LQMNSLTPED TAVYYCAREQ AVGTNPWAFD YWGQGTLVTV SS |
-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: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: HIVMTQSPLS LSVTPGQPAS ISCKSSQISS WGSDGKTYLY WYLQKPGQSP QLLIYEVSSR FSGVSDRFSG SGSGTDFTLK ISRVQAEDVG LYYCMQGLHL PLTFGQGTRL EIK |
-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-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. The complex was further incubated at 37 deg C for 30 min, and then incubated at 4 deg C for another 2 h |
-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: FIELD EMISSION GUN |
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 |
-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: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 23584 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |