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Yorodumi- EMDB-44736: HIV Envelope trimer BG505 SOSIP.664 in complex with wild type CH1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44736 | |||||||||
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Title | HIV Envelope trimer BG505 SOSIP.664 in complex with wild type CH103 antibody | |||||||||
Map data | HIV Envelope BG505 SOSIP.664 trimer in in complex with CH103 wild-type antibody. | |||||||||
Sample |
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Keywords | HIV Envelope Antibody Complex / VIRAL PROTEIN | |||||||||
Biological species | Human immunodeficiency virus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 13.0 Å | |||||||||
Authors | Edwards RJ / Mansouri K | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Acquisition of Quaternary Interaction during Lineage Maturation Increases the Potency of an HIV-1 Broadly Neutralizing Antibody Authors: Liu Q / Parsons R / Wiehe K / Edwards RJ / Saunders KO / Zhang P / Miao H / Williams W / Huang X / Janowska K / Mansouri K / Acharya P / Haynes BF / Lusso P | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44736.map.gz | 14 MB | EMDB map data format | |
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Header (meta data) | emd-44736-v30.xml emd-44736.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44736_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_44736.png | 53 KB | ||
Filedesc metadata | emd-44736.cif.gz | 4.9 KB | ||
Others | emd_44736_half_map_1.map.gz emd_44736_half_map_2.map.gz | 11.8 MB 11.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44736 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44736 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_44736.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | HIV Envelope BG505 SOSIP.664 trimer in in complex with CH103 wild-type antibody. | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.12 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map of BG505-CH103 WT complex
File | emd_44736_half_map_1.map | ||||||||||||
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Annotation | Half-map of BG505-CH103 WT complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map of BG505-CH103 WT complex
File | emd_44736_half_map_2.map | ||||||||||||
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Annotation | Half-map of BG505-CH103 WT complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of BG505 SOSIP.664 with two CH103 wildtype Fabs
Entire | Name: Complex of BG505 SOSIP.664 with two CH103 wildtype Fabs |
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Components |
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-Supramolecule #1: Complex of BG505 SOSIP.664 with two CH103 wildtype Fabs
Supramolecule | Name: Complex of BG505 SOSIP.664 with two CH103 wildtype Fabs type: complex / ID: 1 / Parent: 0 |
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Molecular weight | Theoretical: 46 KDa |
-Supramolecule #2: BG505 SOSIP Trimer
Supramolecule | Name: BG505 SOSIP Trimer / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Human immunodeficiency virus 2 / Strain: BG505 |
-Supramolecule #3: CH103 wildtype Fab
Supramolecule | Name: CH103 wildtype Fab / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #4: CH103 wildtype Fab
Supramolecule | Name: CH103 wildtype Fab / type: complex / ID: 4 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Staining | Type: NEGATIVE / Material: uranyl formate Details: Quenched sample was applied to a glow-discharged carbon-coated 300 mesh EM grid for 10 seconds, blotted and stained with 2 g/dL uranyl formate for 1 minute, blotted and air dried. | ||||||||||||
Grid | Model: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. | ||||||||||||
Details | Complex formed by incubating 20 micrograms trimer with 36 micrograms Fab overnight at 4 degrees C, followed by SEC purification over a Superose 6 Increase 10 300 column. Purified complex was concentrated to 1-2 mg/ml with a 100 kDA spin concentrator, then diluted with buffer containing 8 mM glutaraldehyde and incubated for 5 minutes. Excess glutaraldehyde was quenched by adding 1 M Tris buffer to a final Tris concentration of 80 mM. |
-Electron microscopy
Microscope | FEI/PHILIPS EM420 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 49000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Image recording | Film or detector model: OTHER / Digitization - Dimensions - Width: 8736 pixel / Digitization - Dimensions - Height: 8740 pixel / Number grids imaged: 1 / Number real images: 130 / Average exposure time: 0.25 sec. / Average electron dose: 32.0 e/Å2 |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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