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Yorodumi- EMDB-7859: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7859 | |||||||||
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Title | Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab | |||||||||
Map data | Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab, primary map | |||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 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_7859.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-7859-v30.xml emd-7859.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7859_fsc.xml | 9 KB | Display | FSC data file |
Images | emd_7859.png | 47.9 KB | ||
Others | emd_7859_half_map_1.map.gz emd_7859_half_map_2.map.gz | 49.5 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7859 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7859 | HTTPS FTP |
-Related structure data
Related structure data | 7858C 7860C 7861C 7862C 7863C 7864C 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_7859.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab, primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in...
File | emd_7859_half_map_1.map | ||||||||||||
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Annotation | Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in...
File | emd_7859_half_map_2.map | ||||||||||||
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Annotation | Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PGT151 Fab and PCT64-35S Fab, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in comp...
Entire | Name: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PCT64-35S Fab and PGT151 Fab |
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Components |
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-Supramolecule #1: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in comp...
Supramolecule | Name: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 in complex with PCT64-35S Fab and PGT151 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: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043
Macromolecule | Name: Full Length HIV-1 Envelope Glycoprotein clone PC64M18C043 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: MKVKGIQMNC QHLLRWGTMI LGLIIICSAA NNLWVTVYYG VPVWRDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPSP QEIHLANVTE KFDMWKNSMV EQMHTDIISL WDESLKPCVK LTPLCITLNC TNITRNVTGG NLTEEGKEEL KNCSFNATTE LRDKIQKVHS ...String: MKVKGIQMNC QHLLRWGTMI LGLIIICSAA NNLWVTVYYG VPVWRDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPSP QEIHLANVTE KFDMWKNSMV EQMHTDIISL WDESLKPCVK LTPLCITLNC TNITRNVTGG NLTEEGKEEL KNCSFNATTE LRDKIQKVHS LFYRLDLVEL NEGNSSDSNT SMYRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC REKEFNGTGP CKKVSTVQCT HGIKPVVSTQ LLLNGSLAEG KVKIRCENIS NNAKTILVQL TTPVRINCTR PSNNTRTSIR IGPGQSFYAT GDIIGDIRKA YCNVSESEWK EALGKVVEQL RNHFNKTITF ASSSGGDLEI TTHSFNCGGE FFYCNTSSLF NSTWDGNSAT NSTQVPNGTI TLPCRIKQII NMWQRTGQAM YAPPIPGKIR CDSNITGLIL IRDGGNNNNE SETFRPGGGD MRNNWRSELY KYKVVKIDPL GVAPTGAKRR VVEREKRAVG IGAVLFGFLG AAGSTMGAAS LTLTVQARQL LSGIVQQQSN LLRAIEAQQH LLRLTVWGIK QLQARVLAVE RYLSDQQLLG IWGCSGKLIC TTNVPWNSSW SNKSQDEIWN NMTWLQWDKE ISNYTDTIYY LIEKSQNQQE VNEKDLLALD KWTNLWNWFG ISNWLWYIRI FIMIVGGLIG LRIIFAVLSV INRVRQGYSP VSFQTLTPNP RELDRPGGIE EGDGELGKTR SIRLVGGFLA LFWDDLRSLC LFSYHRLRDF ILIAARILEL LGHNSLKGLR LGWEGLKYLG NLLLYWGREL KNSAVNLVDT IAIVVAGWTD RVIEVLQGIG RAFLHIPRRI RQGFERALL |
-Macromolecule #2: Immunoglobulin G PGT151 Fab, Heavy chain
Macromolecule | Name: Immunoglobulin G PGT151 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: RVQLVESGGG VVQPGKSVRL SCVVSDFPFS KYPMYWVRQA PGKGLEWVAA ISGDAWHVVY SNSVQGRFLV SRDNVKNTLY LEMNSLKIE DTAVYRCARM FQESGPPRLD RWSGRNYYYY SGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA L GCLVKDYF ...String: RVQLVESGGG VVQPGKSVRL SCVVSDFPFS KYPMYWVRQA PGKGLEWVAA ISGDAWHVVY SNSVQGRFLV SRDNVKNTLY LEMNSLKIE DTAVYRCARM FQESGPPRLD RWSGRNYYYY SGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA L GCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DK |
-Macromolecule #3: Immunoglobulin G PGT151, Light chain
Macromolecule | Name: Immunoglobulin G PGT151, 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: DIVMTQTPLS LSVTPGQPAS ISCKSSESLR QSNGKTSLYW YRQKPGQSPQ LLVFEVSNRF SGVSDRFVGS GSGTDFTLRI SRVEAEDVG FYYCMQSKDF PLTFGGGTKV DLKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String: DIVMTQTPLS LSVTPGQPAS ISCKSSESLR QSNGKTSLYW YRQKPGQSPQ LLVFEVSNRF SGVSDRFVGS GSGTDFTLRI SRVEAEDVG FYYCMQSKDF PLTFGGGTKV DLKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C |
-Macromolecule #4: Immunoglobulin G PCT64_35S Fab, Heavy chain
Macromolecule | Name: Immunoglobulin G PCT64_35S Fab, Heavy chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LVKPGGSLRL ACVGSEFTFS EAWMTWVRQA PGKGLEWVGH MRPTTEGGAK DYAAAVRGRF TIARDDSKST LYLQMNSLKI EDTGVYYCMT GVERGDFWSD DYSQHYNTYL IDVWGKGTTV TVSS |
-Macromolecule #5: Immunoglobulin G PCT64_35S, Light chain
Macromolecule | Name: Immunoglobulin G PCT64_35S, Light chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSPGDRAT LSCRATQSVG GDYFAWYQQR PGQSPRLLIY GTSRRAAGIP DRFSGSGSG TDFTLTIDRL EPEDFAVYYC RQYETSFTFG PGTKVDIK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER / Details: Specimen was manually frozen. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 980 / Average electron dose: 37.5 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |