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- EMDB-7858: Ectodomain of full length, wild type HIV-1 glycoprotein clone PC6... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7858 | ||||||||||||
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Title | Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab | ||||||||||||
![]() | Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab | ||||||||||||
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Function / homology | ![]() virus-mediated perturbation of host defense response => GO:0019049 / immunoglobulin complex, circulating / immunoglobulin receptor binding / host cell endosome membrane / complement activation, classical pathway / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / blood microparticle ...virus-mediated perturbation of host defense response => GO:0019049 / immunoglobulin complex, circulating / immunoglobulin receptor binding / host cell endosome membrane / complement activation, classical pathway / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / blood microparticle / immune response / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / extracellular space / extracellular exosome / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
![]() | Berndsens ZB / Rantalainen KR / Ward AB | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.6 KB 22.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.3 KB | Display | ![]() |
Images | ![]() | 382.1 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Others | ![]() ![]() | 98.2 MB 98.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 810 KB | Display | ![]() |
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Full document | ![]() | 809.6 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dcqMC ![]() 7859C ![]() 7860C ![]() 7861C ![]() 7862C ![]() 7863C ![]() 7864C ![]() 7865C ![]() 7866C ![]() 6ca6C ![]() 6ca7C ![]() 6ca9C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
-Half map: Ectodomain of full length, wild type HIV-1 glycoprotein...
File | emd_7858_half_map_1.map | ||||||||||||
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Annotation | Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Ectodomain of full length, wild type HIV-1 glycoprotein...
File | emd_7858_half_map_2.map | ||||||||||||
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Annotation | Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Full length, wild type HIV-1 Envelope glycoprotein in complex wit...
Entire | Name: Full length, wild type HIV-1 Envelope glycoprotein in complex with PGT151 Fab |
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Components |
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-Supramolecule #1: Full length, wild type HIV-1 Envelope glycoprotein in complex wit...
Supramolecule | Name: Full length, wild type HIV-1 Envelope glycoprotein in complex with PGT151 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Full length HIV-1 Envelope glycoprotein clone C043 collected 18 months post infection from donor 64 of Protocol C cohort study. Expressed as recombinant protein in HEK293F cell line. |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 389 KDa |
-Macromolecule #1: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 53.392359 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: SAANNLWVTV YYGVPVWRDA ETTLFCASDA KAYDTEVHNV WATHACVPTD PSPQEIHLAN VTEKFDMWKN SMVEQMHTDI ISLWDESLK PCVKLTPLCI TLNCTNITRN VTGGNLTEEG KEELKNCSFN ATTELRDKIQ KVHSLFYRLD LVELNEGNSS D SNTSMYRL ...String: SAANNLWVTV YYGVPVWRDA ETTLFCASDA KAYDTEVHNV WATHACVPTD PSPQEIHLAN VTEKFDMWKN SMVEQMHTDI ISLWDESLK PCVKLTPLCI TLNCTNITRN VTGGNLTEEG KEELKNCSFN ATTELRDKIQ KVHSLFYRLD LVELNEGNSS D SNTSMYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCREKEF NGTGPCKKVS TVQCTHGIKP VVSTQLLLNG SL AEGKVKI RCENISNNAK TILVQLTTPV RINCTRPSNN TRTSIRIGPG QSFYATGDII GDIRKAYCNV SESEWKEALG KVV EQLRNH FNKTITFASS SGGDLEITTH SFNCGGEFFY CNTSSLFNST WDGNSATNST QVPNGTITLP CRIKQIINMW QRTG QAMYA PPIPGKIRCD SNITGLILIR DGGNNNNESE TFRPGGGDMR NNWRSELYKY KVVKIDPLGV APTGAKRRVV EREKR |
-Macromolecule #2: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 40.020207 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AVGIGAVLFG FLGAAGSTMG AASLTLTVQA RQLLSGIVQQ QSNLLRAIEA QQHLLRLTVW GIKQLQARVL AVERYLSDQQ LLGIWGCSG KLICTTNVPW NSSWSNKSQD EIWNNMTWLQ WDKEISNYTD TIYYLIEKSQ NQQEVNEKDL LALDKWTNLW N WFGISNWL ...String: AVGIGAVLFG FLGAAGSTMG AASLTLTVQA RQLLSGIVQQ QSNLLRAIEA QQHLLRLTVW GIKQLQARVL AVERYLSDQQ LLGIWGCSG KLICTTNVPW NSSWSNKSQD EIWNNMTWLQ WDKEISNYTD TIYYLIEKSQ NQQEVNEKDL LALDKWTNLW N WFGISNWL WYIRIFIMIV GGLIGLRIIF AVLSVINRVR QGYSPVSFQT LTPNPRELDR PGGIEEGDGE LGKTRSIRLV GG FLALFWD DLRSLCLFSY HRLRDFILIA ARILELLGHN SLKGLRLGWE GLKYLGNLLL YWGRELKNSA VNLVDTIAIV VAG WTDRVI EVLQGIGRAF LHIPRRIRQG FERALL |
-Macromolecule #3: Immunoglobulin G PGT151 Fab, Heavy chain
Macromolecule | Name: Immunoglobulin G PGT151 Fab, Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.087438 KDa |
Recombinant expression | Organism: ![]() |
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 #4: Immunoglobulin G PGT151 Fab, Light chain
Macromolecule | Name: Immunoglobulin G PGT151 Fab, Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.057809 KDa |
Recombinant expression | Organism: ![]() |
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 #14: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 14 / Number of copies: 21 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 7 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
Details: Detergent removed with Biobeads prior to grid freezing | |||||||||||||||
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 0 Blot time 5 sec. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4039 / Average electron dose: 1.885 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |