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- PDB-8jn7: Cryo-EM structure of the big tail club shape particle of dengue v... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jn7 | ||||||
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Title | Cryo-EM structure of the big tail club shape particle of dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C | ||||||
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![]() | VIRUS/IMMUNE SYSTEM / dengue virus / human antibody / dengue-antibody structure / virus / VIRUS-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 11 Å | ||||||
![]() | Fibriansah, G. / Ng, T.S. / Tan, A.W.K. / Shi, J. / Lok, S.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Ultrapotent human antibodies lock E protein dimers of diverse DENV3 morphological variants Authors: Fibriansah, G. / Ng, T.S. / Lim, X.N. / Shebanova, A. / Ng, L.C. / Tan, S.L. / Tan, A.W.K. / Shi, J. / Crowe, J.E.J. / Lok, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 33.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 36435MC ![]() 8jn1C ![]() 8jn2C ![]() 8jn3C ![]() 8jn4C ![]() 8jn5C ![]() 8jn6C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Components
#1: Protein | Mass: 53730.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | | Mass: 13495.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | | Mass: 12381.966 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: helical reconstruction |
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Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Details of virus |
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Buffer solution | pH: 8 Details: NTE buffer (12 mM Tris-HCl pH 8.0, 120 mM NaCl and 1 mM EDTA) | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES 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 ...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 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 18 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 128.09 ° / Axial rise/subunit: 10.7 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35641 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building |
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