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Yorodumi- EMDB-7861: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in compl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7861 | |||||||||
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Title | Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64-13C Fab | |||||||||
Map data | Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and 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_7861.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-7861-v30.xml emd-7861.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7861_fsc.xml | 4.3 KB | Display | FSC data file |
Images | emd_7861.png | 46.7 KB | ||
Others | emd_7861_half_map_1.map.gz emd_7861_half_map_2.map.gz | 2.8 MB 2.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7861 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7861 | HTTPS FTP |
-Related structure data
Related structure data | 7858C 7859C 7860C 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_7861.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64-13C Fab, primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in...
File | emd_7861_half_map_1.map | ||||||||||||
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Annotation | Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64-13C Fab, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in...
File | emd_7861_half_map_2.map | ||||||||||||
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Annotation | Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64-13C Fab, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in compl...
Entire | Name: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and PCT64_13C Fab |
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Components |
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-Supramolecule #1: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in compl...
Supramolecule | Name: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 in complex with PGT151 Fab and 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: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054
Macromolecule | Name: Full length HIV-1 Envelope Glycoprotein clone PC64M4C054 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: MKVRGIQMNC QHLLRWGTMI LGLIIICSAA NNLWVTVYYG VPVWRDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPSP QEIHLANVTE KFNMWKNSMV EQMHTDIISL WDESLKPCVK LTPLCITLNC TNITRKNVTG GNLTEDGKEE LKNCSFNATT ELRNKRQKVH ...String: MKVRGIQMNC QHLLRWGTMI LGLIIICSAA NNLWVTVYYG VPVWRDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPSP QEIHLANVTE KFNMWKNSMV EQMHTDIISL WDESLKPCVK LTPLCITLNC TNITRKNVTG GNLTEDGKEE LKNCSFNATT ELRNKRQKVH SLFYRLDLVE LNEGNSSNSN TSMYRLINCN TSAITQACPK VSFEPIPIHY CAPAGFAILK CREEEFNGTG PCKNVSTVQC THGIKPVVST QLLLNGSLAE GTVKIRCENI SNNAKTILVQ LTTPVRINCT RPNNNTRTSI RIGPGQSFYA TGDIIGDIRK AYCNVSGSEW KEALGKVVVQ LRSHFNKTIT FASSSGGDLE ITTHSFNCGG EFFYCNTSSL FNSTWDGNST TNSTQEPNGT ITLPCRIKQI INMWQRTGQA MYAPPIPGKI RCDSNITGLI LTRDGENNNT ESETFRPEGG DMRNNWRSEL YKYKVVKIDP LGVAPTGAKR RVVEREKRAV GIGAVLFGFL GAAGSTMGAA SLTLTVQARQ LLSGIVQQQS NLLRAIEAQQ HLLRLTVWGI KQLQARVLAV ERYLSDQQLL GIWGCSGKLI CTTTVPWNSS WSNKSQDEIW NNMTWLQWDK EISNYTDTIY YLIEKSQNQQ EVNEKDLLAL DKWTNLWNWF DISKWLWYIK IFIMIVGGLI GLRIIFAVLS VINRVRQGYP PVSFQTLTPN PRELDRPGGI EEGDGELGKT RSIRLVGGFL ALFWDDLRSL CLFSYHRLRD FSLIAARILE LLGHNSLKGL RLGWEGLKYL GNLLLYWGRE LKNSAVNLVD TIAIVVAGWT DRVIEVLQGI GRAFLHIPRR IRQGLERALL |
-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_13C Fab, Heavy chain
Macromolecule | Name: Immunoglobulin G PCT64_13C 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 SCAASGFTFT NAWLDWVRQA PGKGLEWVGR IKSKTDGGTT DHAAPVKGRF TISRDDSKNT VYLQMNSLKI EDTAVYYCTT GVETYDFWSG YDDHYYDYYF KDVWGKGTTV TVSS |
-Macromolecule #5: Immunoglobulin G PCT64_13C, Light chain
Macromolecule | Name: Immunoglobulin G PCT64_13C, 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 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: uranyl formate |
Grid | Material: COPPER / Pretreatment - Type: PLASMA CLEANING |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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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 |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 222 / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |