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- EMDB-7865: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP in complex wit... -
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Open data
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Basic information
Entry | Database: EMDB / ID: 7865 |
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Title | HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP in complex with PCT64-35S Fab |
![]() | HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP in complex with PCT64-35S Fab, primary map |
![]() | HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64-35S Fab
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Source | ![]() ![]() ![]() ![]() ![]() |
Method | ![]() ![]() |
![]() | Berndsens ZB / Rantalainen KR / Ward AB |
![]() | Journal: Cell Rep / Year: 2018 Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design. ![]() Abstract: Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at ...Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex. |
Date | Deposition: May 9, 2018 / Header (metadata) release: May 30, 2018 / Map release: Jun 27, 2018 / Last update: Jun 27, 2018 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
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Header (meta data in XML format) | ![]() ![]() ![]() |
FSC (resolution estimation) | ![]() |
Images | ![]() |
Masks (Map data of sub-region, etc) | ![]() |
Others | ![]() ![]() |
FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7865 |
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Links
-Related structure data
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex...
Entire | Name: HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64-35S Fab Number of components: 4 |
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-Component #1: protein, HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 i...
Protein | Name: HIV-1 Envelope glycoprotein clone PC64M4C054.SOSIP.664 in complex with PCT64-35S Fab Recombinant expression: No |
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Source | Species: ![]() ![]() |
-Component #2: protein, HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664
Protein | Name: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664 Recombinant expression: No |
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Source | Species: ![]() ![]() ![]() |
Source (engineered) | Expression System: ![]() ![]() |
-Component #3: protein, Immunoglobulin G PCT64-35S Fab, Heavy chain
Protein | Name: Immunoglobulin G PCT64-35S Fab, Heavy chain / Recombinant expression: No |
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Source | Species: ![]() ![]() |
Source (engineered) | Expression System: ![]() ![]() |
-Component #4: protein, Immunoglobulin G PCT64-35S Fab, Light chain
Protein | Name: Immunoglobulin G PCT64-35S Fab, Light chain / Recombinant expression: No |
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Source | Species: ![]() ![]() |
Source (engineered) | Expression System: ![]() ![]() |
-Experimental details
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Sample preparation
Specimen | Specimen state: particle / Method: ![]() |
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Sample solution | pH: 7.4 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 % / Details: Blot force 0 Blot time 5 sec. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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![]() | Microscope: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Cs: 2.7 mm / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: OTHER |
Camera | Detector: GATAN K2 SUMMIT (4k x 4k) |
-Image acquisition
Image acquisition | Number of digital images: 2007 |
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