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Yorodumi- EMDB-8950: Cryo-EM structure at 3.5 A resolution of vaccine-elicited, fusion... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8950 | |||||||||
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Title | Cryo-EM structure at 3.5 A resolution of vaccine-elicited, fusion peptide-directed antibody OPV-d.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122 | |||||||||
Map data | Map after refinement in cryosparc and post processing in Relion using the tight mask from cryosparc that was autogenerated for FSC autotightening. | |||||||||
Sample |
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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 | Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Acharya P / Kwong PD | |||||||||
Citation | Journal: To Be Published Title: Cryo-EM structure at 3.5 A resolution of vaccine-elicited, fusion peptide-directed antibody OPV21 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122 Authors: Acharya P / Kwong PD | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8950.map.gz | 14.3 MB | EMDB map data format | |
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Header (meta data) | emd-8950-v30.xml emd-8950.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8950_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_8950.png | 104 KB | ||
Masks | emd_8950_msk_1.map emd_8950_msk_2.map | 216 MB 216 MB | Mask map | |
Others | emd_8950_additional.map.gz emd_8950_half_map_1.map.gz emd_8950_half_map_2.map.gz | 20.3 MB 200.3 MB 200.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8950 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8950 | HTTPS FTP |
-Validation report
Summary document | emd_8950_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_8950_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_8950_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8950 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8950 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8950.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map after refinement in cryosparc and post processing in Relion using the tight mask from cryosparc that was autogenerated for FSC autotightening. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0605 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_8950_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_8950_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Map generated after postprocessing in RELION using the...
File | emd_8950_additional.map | ||||||||||||
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Annotation | Map generated after postprocessing in RELION using the looser mask generated in CryoSparc (used in the final iteration of cryoSparc refinement) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_8950_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_8950_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Quaternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of...
Entire | Name: Quaternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies OPV21, VRC03 and PGT122. |
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Components |
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-Supramolecule #1: Quaternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of...
Supramolecule | Name: Quaternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies OPV21, VRC03 and PGT122. type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.01 |
Grid | Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: SPOTITON |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2700 / Average exposure time: 10.0 sec. / Average electron dose: 95.8 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: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 156 |
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