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- EMDB-42516: HIV-1 JR-FL NFL.664 soluble trimer in complex with polyclonal Fab... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | HIV-1 JR-FL NFL.664 soluble trimer in complex with polyclonal Fab from rabbit U5902 | |||||||||
![]() | main map | |||||||||
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![]() | EMPEM / polyclonal antibodies / rabbit / HIV vaccine candidate / HIV-1 / Env / VIRAL PROTEIN | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 29.0 Å | |||||||||
![]() | Lee W-H / Ozorowski G / Ward AB | |||||||||
Funding support | ![]()
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![]() | ![]() Title: mRNA lipid nanoparticles expressing cell-surface cleavage independent HIV Env trimers elicit autologous tier-2 neutralizing antibodies Authors: Guenaga J / Alirezaei M / Feng Y / Alameh M-G / Lee W-H / Baboo S / Cluff J / Wilson R / Bale S / Ozorowski G / Lin P / Tam Y / Diedrich JK / Yates JR / Paulson J / Ward AB / Weissman D / Wyatt RT | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.2 KB 14.2 KB | Display Display | ![]() |
Images | ![]() | 54.7 KB | ||
Filedesc metadata | ![]() | 4.2 KB | ||
Others | ![]() ![]() | 20.6 MB 20.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 736.2 KB | Display | ![]() |
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Full document | ![]() | 735.7 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.68 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B
File | emd_42516_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_42516_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : HIV-1 JR-FL NFL.664 soluble trimer in complex with polyclonal Fab...
Entire | Name: HIV-1 JR-FL NFL.664 soluble trimer in complex with polyclonal Fab from rabbit U5902 |
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Components |
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-Supramolecule #1: HIV-1 JR-FL NFL.664 soluble trimer in complex with polyclonal Fab...
Supramolecule | Name: HIV-1 JR-FL NFL.664 soluble trimer in complex with polyclonal Fab from rabbit U5902 type: complex / ID: 1 / Parent: 0 / Details: HIV-1 JR-FL NFL.664 soluble trimer |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: HIV-1 JR-FL NFL.664 soluble trimer in complex with polyclonal Fab...
Supramolecule | Name: HIV-1 JR-FL NFL.664 soluble trimer in complex with polyclonal Fab from rabbit U5902 type: complex / ID: 2 / Parent: 1 / Details: polyclonal Fab from rabbit U5902 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.4 |
Staining | Type: NEGATIVE / Material: uranyl formate / Details: 2% w/v |
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: EM map simulated from coordinates using molmap in UCSF Chimera and low pass filtered |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 1651 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |