+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7105 | |||||||||
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Title | HIV-1 Envelope Glycoprotein clone PC64M7c022 SOSIP.664 | |||||||||
Map data | primary map | |||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 26.0 Å | |||||||||
Authors | Berndsen ZT / Rantalainen K / Ward AB | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Immunity / Year: 2017 Title: HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage. Authors: Elise Landais / Ben Murrell / Bryan Briney / Sasha Murrell / Kimmo Rantalainen / Zachary T Berndsen / Alejandra Ramos / Lalinda Wickramasinghe / Melissa Laird Smith / Kemal Eren / Natalia de ...Authors: Elise Landais / Ben Murrell / Bryan Briney / Sasha Murrell / Kimmo Rantalainen / Zachary T Berndsen / Alejandra Ramos / Lalinda Wickramasinghe / Melissa Laird Smith / Kemal Eren / Natalia de Val / Mengyu Wu / Audrey Cappelletti / Jeffrey Umotoy / Yolanda Lie / Terri Wrin / Paul Algate / Po-Ying Chan-Hui / Etienne Karita / / / Andrew B Ward / Ian A Wilson / Dennis R Burton / Davey Smith / Sergei L Kosakovsky Pond / Pascal Poignard / Abstract: Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb ...Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb lineage targeting the Env V2 apex and the Ab-Env co-evolution that led to development of neutralization breadth. The lineage Abs bore an anionic heavy chain complementarity-determining region 3 (CDRH3) of 25 amino acids, among the shortest known for this class of Abs, and achieved breadth with only 10% nucleotide somatic hypermutation and no insertions or deletions. The data suggested a role for Env glycoform heterogeneity in the activation of the lineage germline B cell. Finally, we showed that localized diversity at key V2 epitope residues drove bnAb maturation toward breadth, mirroring the Env evolution pattern described for another donor who developed V2-apex targeting bnAbs. Overall, these findings suggest potential strategies for vaccine approaches based on germline-targeting and serial immunogen design. | |||||||||
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_7105.map.gz | 734.6 KB | EMDB map data format | |
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Header (meta data) | emd-7105-v30.xml emd-7105.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7105_fsc.xml | 2.8 KB | Display | FSC data file |
Images | emd_7105.png | 53.6 KB | ||
Masks | emd_7105_msk_1.map | 1 MB | Mask map | |
Others | emd_7105_half_map_1.map.gz emd_7105_half_map_2.map.gz | 740.9 KB 739.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7105 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7105 | HTTPS FTP |
-Validation report
Summary document | emd_7105_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_7105_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_7105_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7105 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7105 | HTTPS FTP |
-Related structure data
Related structure data | 7089C 7104C 7106C 7107C 7108C 5fehC 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_7105.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 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
-Mask #1
File | emd_7105_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_7105_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_7105_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 Envelope Glycoprotein clone PC64M7c022 SOSIP.664
Entire | Name: HIV-1 Envelope Glycoprotein clone PC64M7c022 SOSIP.664 |
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Components |
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-Supramolecule #1: HIV-1 Envelope Glycoprotein clone PC64M7c022 SOSIP.664
Supramolecule | Name: HIV-1 Envelope Glycoprotein clone PC64M7c022 SOSIP.664 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) |
Molecular weight | Theoretical: 225 KDa |
-Macromolecule #1: HIV-1 Envelope Glycoprotein PC64M7c022 SOSIP.664
Macromolecule | Name: HIV-1 Envelope Glycoprotein PC64M7c022 SOSIP.664 / 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 RRGAR ANNL WVTVYYGVPV WRDAETTLFC ASDAKAYDTE VHNVWATHAC VPTDPSPQEI HLANVTEKFD MWKNSMVEQM HTDIISLWDE SLKPCVKLTP LCITLNCTNI TKKNVTGGNL TEDGKEELKN CSFNATTELS ...String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGAR ANNL WVTVYYGVPV WRDAETTLFC ASDAKAYDTE VHNVWATHAC VPTDPSPQEI HLANVTEKFD MWKNSMVEQM HTDIISLWDE SLKPCVKLTP LCITLNCTNI TKKNVTGGNL TEDGKEELKN CSFNATTELS NKRQKVHSLF YRLDLVELNE GNSSNSNTSM YRLINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCRE KEFNGTGPCK NVSTVQCTHG IKPVVSTQLL LNGSLAEGTV KIRCENISNN AKTILVQLTT PVRINCTRPN NNTRTSIRIG PGQSFYATGD IIGDIRKAYC NVSGSEWKEA LGKVVVQLRN HFNKTITFAS SSGGDLEITT HSFNCGGEFF YCNTSSLFNS TWDRNSTTNS TQEPNGTITL PCRIKQIINM WQRTGQAMYA PPIPGKIRCD SNITGLILTR DGENNNTESE TFRPEGGDMR NNWRSELYKY KVVKIDPLGV APTGCKRRVV ERRRRRRAVG IGAVLFGFLG AAGSTMGAAS LTLTVQARQL LSGIVQQQSN LLRAPEAQQH LLRLTVWGIK QLQARVLAVE RYLSDQQLLG IWGCSGKLIC CTTVPWNSSW SNKSQDEIWN NMTWLQWDKE ISNYTDTIYY LIEKSQNQQE VNEKDLLALD KWTNLWNWFD ISKWLWYIKI FIMIVGGLIG LRIIFAVLSV INRVRQGYSP VSFQTLTPNP RELDRPGGIE EGDGELGKTR SIRLVGGFLA LFWDDLRSLC LFSYHRLRDF ILIAARILEL LGHNSLKGLR LGWEGLKYLG NLLLYWGREL KNSAVNLVDT IAIVVAGWTD RVIEVLQGIG RAFLHVPRRI RQGLERALL |
-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: NanoW |
Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average exposure time: 0.5 sec. / 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 |