+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8168 | |||||||||
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Title | BF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer | |||||||||
Map data | BF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer | |||||||||
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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 10.9 Å | |||||||||
Authors | Williams JA / Lee KK | |||||||||
Citation | Journal: Cell / Year: 2016 Title: HIV-1 Neutralizing Antibodies with Limited Hypermutation from an Infant. Authors: Cassandra A Simonich / Katherine L Williams / Hans P Verkerke / James A Williams / Ruth Nduati / Kelly K Lee / Julie Overbaugh / Abstract: HIV-1 broadly neutralizing antibodies (bnAbs) develop in a subset of infected adults and exhibit high levels of somatic hypermutation (SHM) due to years of affinity maturation. There is no precedent ...HIV-1 broadly neutralizing antibodies (bnAbs) develop in a subset of infected adults and exhibit high levels of somatic hypermutation (SHM) due to years of affinity maturation. There is no precedent for eliciting highly mutated antibodies by vaccination, nor is it practical to wait years for a desired response. Infants develop broad responses early, which may suggest a more direct path to generating bnAbs. Here, we isolated ten neutralizing antibodies (nAbs) contributing to plasma breadth of an infant at ∼1 year post-infection, including one with cross-clade breadth. The nAbs bind to envelope trimer from the transmitted virus, suggesting that this interaction may have initiated development of the infant nAbs. The infant cross-clade bnAb targets the N332 supersite on envelope but, unlike adult bnAbs targeting this site, lacks indels and has low SHM. The identification of this infant bnAb illustrates that HIV-1-specific neutralization breadth can develop without prolonged affinity maturation and extensive SHM. | |||||||||
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_8168.map.gz | 484.5 KB | EMDB map data format | |
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Header (meta data) | emd-8168-v30.xml emd-8168.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8168_fsc.xml | 3.6 KB | Display | FSC data file |
Images | emd_8168.png | 60 KB | ||
Others | emd_8168_half_map_1.map.gz emd_8168_half_map_2.map.gz | 476.9 KB 474.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8168 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8168 | 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_8168.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | BF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: BF520.1 Fab fragment bound to BG505 T332N SOSIP.664...
File | emd_8168_half_map_1.map | ||||||||||||
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Annotation | BF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: BF520.1 Fab fragment bound to BG505 T332N SOSIP.664...
File | emd_8168_half_map_2.map | ||||||||||||
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Annotation | BF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
Entire | Name: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer |
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Components |
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-Supramolecule #1: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
Supramolecule | Name: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #2: BF520.1 Fab
Supramolecule | Name: BF520.1 Fab / type: complex / ID: 2 / Parent: 1 Details: Fab domains generated by papain digestion of BF520.1 IgG |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: BG505.C2 T332N SOSIP.664 trimer
Supramolecule | Name: BG505.C2 T332N SOSIP.664 trimer / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: BG505.C2 T332N |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK 293F / Recombinant plasmid: pPPI4 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.020 mg/mL |
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Buffer | pH: 7.5 |
Staining | Type: NEGATIVE / Material: methylamine tungstate |
Grid | Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 24.0 e/Å2 |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |