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Yorodumi- EMDB-8420: Cryo-EM structure of BG505 DS-SOSIP HIV-1 Env trimer in complex w... -
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-Basic information
Entry | Database: EMDB / ID: EMD-8420 | |||||||||
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Title | Cryo-EM structure of BG505 DS-SOSIP HIV-1 Env trimer in complex with vaccine elicited, fusion peptide-directed antibody vFP1.01 | |||||||||
Map data | Single particle cryo-EM reconstruction of stabilized BG505 SOSIP in complex with vaccine elicited fusion peptide directed antibody FP1 | |||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.58 Å | |||||||||
Authors | Acharya P / Kwong PD / Potter CS / Carragher B | |||||||||
Citation | Journal: Nat Med / Year: 2018 Title: Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1. Authors: Kai Xu / Priyamvada Acharya / Rui Kong / Cheng Cheng / Gwo-Yu Chuang / Kevin Liu / Mark K Louder / Sijy O'Dell / Reda Rawi / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou ...Authors: Kai Xu / Priyamvada Acharya / Rui Kong / Cheng Cheng / Gwo-Yu Chuang / Kevin Liu / Mark K Louder / Sijy O'Dell / Reda Rawi / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Mangaiarkarasi Asokan / Robert T Bailer / Michael Chambers / Xuejun Chen / Chang W Choi / Venkata P Dandey / Nicole A Doria-Rose / Aliaksandr Druz / Edward T Eng / S Katie Farney / Kathryn E Foulds / Hui Geng / Ivelin S Georgiev / Jason Gorman / Kurt R Hill / Alexander J Jafari / Young D Kwon / Yen-Ting Lai / Thomas Lemmin / Krisha McKee / Tiffany Y Ohr / Li Ou / Dongjun Peng / Ariana P Rowshan / Zizhang Sheng / John-Paul Todd / Yaroslav Tsybovsky / Elise G Viox / Yiran Wang / Hui Wei / Yongping Yang / Amy F Zhou / Rui Chen / Lu Yang / Diana G Scorpio / Adrian B McDermott / Lawrence Shapiro / Bridget Carragher / Clinton S Potter / John R Mascola / Peter D Kwong / Abstract: A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N- ...A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion stabilized envelope trimers, induces cross-clade neutralizing responses. In mice, these immunogens elicited monoclonal antibodies capable of neutralizing up to 31% of a cross-clade panel of 208 HIV-1 strains. Crystal and cryoelectron microscopy structures of these antibodies revealed fusion peptide conformational diversity as a molecular explanation for the cross-clade neutralization. Immunization of guinea pigs and rhesus macaques induced similarly broad fusion peptide-directed neutralizing responses, suggesting translatability. The N terminus of the HIV-1 fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies. | |||||||||
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_8420.map.gz | 116.5 MB | EMDB map data format | |
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Header (meta data) | emd-8420-v30.xml emd-8420.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8420_fsc.xml | 11 KB | Display | FSC data file |
Images | emd_8420.png | 145.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8420 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8420 | HTTPS FTP |
-Related structure data
Related structure data | 7459C 7460C 8421C 8422C 5tkjC 5tkkC 6cdeC 6cdiC 6cdmC 6cdoC 6cdpC 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_8420.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Single particle cryo-EM reconstruction of stabilized BG505 SOSIP in complex with vaccine elicited fusion peptide directed antibody FP1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : HIV-1 Env trimer
Entire | Name: HIV-1 Env trimer |
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Components |
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-Supramolecule #1: HIV-1 Env trimer
Supramolecule | Name: HIV-1 Env trimer / 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 plasmid: pVRC8400 |
-Supramolecule #2: HIV-1 Env trimer in complex with antibody
Supramolecule | Name: HIV-1 Env trimer in complex with antibody / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant plasmid: pVRC8400 |
-Macromolecule #1: BG505 DS-SOSIP
Macromolecule | Name: BG505 DS-SOSIP / 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: SRATMPMGSL QPLATLYLLG MLVASVLAAE NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ KVYSLFYRLD ...String: SRATMPMGSL QPLATLYLLG MLVASVLAAE NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ KVYSLFYRLD VVQINENQGN RSNNSNKEYR LINCNTSAcT QACPKVSFEP IPIHYCAPAG FAILKCKDKK FNGTGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAFYATGDII GDIRQAHCNV SKATWNETLG KVVKQLRKHF GNNTIIRFAN SSGGDLEVTT HSFNCGGEFF YCNTSGLFNS TWISNTSVQG SNSTGSNDSI TLPCRIKQII NMWQRIGQcM YAPPIQGVIR CVSNITGLIL TRDGGSTNST TETFRPGGGD MRDNWRSELY KYKVVKIEPL GVAPTRCKRR VVGRRRRRRA VGIGAVFLGF LGAAGSTMGA ASMTLTVQAR NLLSGIVQQQ SNLLRAPEAQ QHLLKLTVWG IKQLQARVLA VERYLRDQQL LGIWGCSGKL ICCTNVPWNS SWSNRNLSEI WDNMTWLQWD KEISNYTQII YGLLEESQNQ QEKNEQDLLA LD |
-Macromolecule #2: vFP1.01 Heavy Chain
Macromolecule | Name: vFP1.01 Heavy Chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: QVQLQQSGTE LVWPGTSVTL SCKASGYTFT DYEIHWVKQT PVHGLEWIGA IVPKTGYTAY NQKFRGKAIL TADKSSSTAY MDLRRLTSE DSAVYYCTRL RNYWYFDVWG TGTTVTVSPA STKGPSVFPL AP |
-Macromolecule #3: vFP1.01 Light chain
Macromolecule | Name: vFP1.01 Light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: DFLMAQTPLS LPVSLGDQAS ISCRSSQSIV YSDGNTYLEW YLQRPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLRI SRVEAEDLG IYYCFQGSHV PYTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String: DFLMAQTPLS LPVSLGDQAS ISCRSSQSIV YSDGNTYLEW YLQRPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLRI SRVEAEDLG IYYCFQGSHV PYTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.2 / Component - Name: HEPES |
Grid | Model: EMS C-flat / Material: COPPER / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 10.0 sec. / Average electron dose: 8.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation Coefficient |
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