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Yorodumi- EMDB-7864: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7864 | |||||||||
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Title | HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab | |||||||||
Map data | HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab, primary map | |||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 30.0 Å | |||||||||
Authors | Berndsen ZT / Rantalainen K / Ward AB | |||||||||
Citation | Journal: Cell Rep / Year: 2018 Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design. Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais ...Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais / James C Paulson / Ian A Wilson / Andrew B Ward / 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. | |||||||||
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_7864.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-7864-v30.xml emd-7864.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7864_fsc.xml | 4.3 KB | Display | FSC data file |
Images | emd_7864.png | 36.1 KB | ||
Others | emd_7864_half_map_1.map.gz emd_7864_half_map_2.map.gz | 2.8 MB 2.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7864 | HTTPS FTP |
-Validation report
Summary document | emd_7864_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_7864_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_7864_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7864 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7864 | HTTPS FTP |
-Related structure data
Related structure data | 7858C 7859C 7860C 7861C 7862C 7863C 7865C 7866C 6ca6C 6ca7C 6ca9C 6dcqC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7864.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab, primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with...
File | emd_7864_half_map_1.map | ||||||||||||
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Annotation | HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with...
File | emd_7864_half_map_2.map | ||||||||||||
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Annotation | HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in c...
Entire | Name: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab |
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Components |
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-Supramolecule #1: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in c...
Supramolecule | Name: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A in complex with PCT64_13C Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F |
-Macromolecule #1: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A
Macromolecule | Name: HIV-1 Envelope Glycoprotein clone PC64M4C054.SOSIP.664.N130A type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARANNLW VTVYYGVPVW RDAETTLFCA SDAKAYDTEV HNVWATHACV PTDPSPQEIH LANVTEKFNM WKNSMVEQMH TDIISLWDES LKPCVKLTPL CITLACTNIT RKNVTGGNLT EDGKEELKNC SFNATTELRN ...String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARANNLW VTVYYGVPVW RDAETTLFCA SDAKAYDTEV HNVWATHACV PTDPSPQEIH LANVTEKFNM WKNSMVEQMH TDIISLWDES LKPCVKLTPL CITLACTNIT RKNVTGGNLT EDGKEELKNC SFNATTELRN KRQKVHSLFY RLDLVELNEG NSSNSNTSMY RLINCNTSAI TQACPKVSFE PIPIHYCAPA GFAILKCREE EFNGTGPCKN VSTVQCTHGI KPVVSTQLLL NGSLAEGTVK IRCENISNNA KTILVQLTTP VRINCTRPNN NTRTSIRIGP GQSFYATGDI IGDIRKAYCN VSGSEWKEAL GKVVVQLRSH FNKTITFASS SGGDLEITTH SFNCGGEFFY CNTSSLFNST WDGNSTTNST QEPNGTITLP CRIKQIINMW QRTGQAMYAP PIPGKIRCDS NITGLILTRD GENNNTESET FRPEGGDMRN NWRSELYKYK VVKIDPLGVA PTGCKRRVVE RRRRRRAVGI GAVLFGFLGA AGSTMGAASL TLTVQARQLL SGIVQQQSNL LRAPEAQQHL LRLTVWGIKQ LQARVLAVER YLSDQQLLGI WGCSGKLICC TTVPWNSSWS NKSQDEIWNN MTWLQWDKEI SNYTDTIYYL IEKSQNQQEV NEKDLLALD |
-Macromolecule #2: Immunoglobulin G PCT64-13C Fab, Heavy chain
Macromolecule | Name: Immunoglobulin G PCT64-13C Fab, Heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LVKPGGSLRL SCAASGFTFT NAWLDWVRQA PGKGLEWVGR IKSKTDGGTT DHAAPVKGRF TISRDDSKNT VYLQMNSLKI EDTAVYYCTT GVETYDFWSG YDDHYYDYYF KDVWGKGTTV TVSS |
-Macromolecule #3: Immunoglobulin G PCT64-13C Fab, Light chain
Macromolecule | Name: Immunoglobulin G PCT64-13C Fab, Light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSPGERAT LSCRASQSVS NNYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSG TDFTLTISRL EPEDFAVYYC QQSARSFTFG PGTKVDIK |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Staining | Type: NEGATIVE / Material: Nano-W |
Grid | Material: COPPER / Pretreatment - Type: PLASMA CLEANING |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 222 / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |