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Yorodumi- EMDB-40797: BG505 GT1.1 SOSIP in complex with NHP Fabs 21N13, 21M20 and RM20A3 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40797 | |||||||||
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Title | BG505 GT1.1 SOSIP in complex with NHP Fabs 21N13, 21M20 and RM20A3 | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Keywords | germline targeting / HIV-1 Env / neutralizing antibody / non-human primate antibody / CD4 binding site / fusion peptide / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Macaca (macaques) / Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||
Authors | Ozorowski G / Torres JL / Zhang S / Ward AB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Neutralizing antibodies induced in non-human primates by germline targeting Env trimer Authors: Caniels T / Ozorowski G / Ward AB / Sanders RW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40797.map.gz | 230.4 MB | EMDB map data format | |
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Header (meta data) | emd-40797-v30.xml emd-40797.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40797_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_40797.png | 102.4 KB | ||
Masks | emd_40797_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-40797.cif.gz | 7.2 KB | ||
Others | emd_40797_half_map_1.map.gz emd_40797_half_map_2.map.gz | 226.9 MB 226.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40797 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40797 | HTTPS FTP |
-Validation report
Summary document | emd_40797_validation.pdf.gz | 1011.5 KB | Display | EMDB validaton report |
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Full document | emd_40797_full_validation.pdf.gz | 1011 KB | Display | |
Data in XML | emd_40797_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | emd_40797_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40797 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40797 | HTTPS FTP |
-Related structure data
Related structure data | 8sw4MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40797.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.044 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40797_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_40797_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_40797_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : BG505 GT1.1 SOSIP in complex with 21N13 Fab, 21M20 Fab and RM20A3 Fab
+Supramolecule #1: BG505 GT1.1 SOSIP in complex with 21N13 Fab, 21M20 Fab and RM20A3 Fab
+Macromolecule #1: 21M20 heavy chain variable region
+Macromolecule #2: 21M20 light chain variable region
+Macromolecule #3: BG505 GT1.1 SOSIP gp120
+Macromolecule #4: Envelope glycoprotein gp41
+Macromolecule #5: RM20A3 heavy chain variable region
+Macromolecule #6: RM20A3 light chain variable region
+Macromolecule #7: 21N13 heavy chain variable region
+Macromolecule #8: 21N13 light chain variable region
+Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: Detergent added shortly before freezing | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 190000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |