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Yorodumi- EMDB-20273: Negative-stain reconstruction of HIV-1 Env BG505 NFL CC+ trimer i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20273 | |||||||||||||||
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Title | Negative-stain reconstruction of HIV-1 Env BG505 NFL CC+ trimer in complex with rabbit antibody E70 fragment antigen binding | |||||||||||||||
Map data | negative-stain 3D reconstruction | |||||||||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 / Oryctolagus cuniculus (rabbit) | |||||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.0 Å | |||||||||||||||
Authors | Torres JL / Ozorowski G / Andrew AB | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Immunity / Year: 2019 Title: Vaccination with Glycan-Modified HIV NFL Envelope Trimer-Liposomes Elicits Broadly Neutralizing Antibodies to Multiple Sites of Vulnerability. Authors: Viktoriya Dubrovskaya / Karen Tran / Gabriel Ozorowski / Javier Guenaga / Richard Wilson / Shridhar Bale / Christopher A Cottrell / Hannah L Turner / Gemma Seabright / Sijy O'Dell / Jonathan ...Authors: Viktoriya Dubrovskaya / Karen Tran / Gabriel Ozorowski / Javier Guenaga / Richard Wilson / Shridhar Bale / Christopher A Cottrell / Hannah L Turner / Gemma Seabright / Sijy O'Dell / Jonathan L Torres / Lifei Yang / Yu Feng / Daniel P Leaman / Néstor Vázquez Bernat / Tyler Liban / Mark Louder / Krisha McKee / Robert T Bailer / Arlette Movsesyan / Nicole A Doria-Rose / Marie Pancera / Gunilla B Karlsson Hedestam / Michael B Zwick / Max Crispin / John R Mascola / Andrew B Ward / Richard T Wyatt / Abstract: The elicitation of broadly neutralizing antibodies (bNAbs) against the HIV-1 envelope glycoprotein (Env) trimer remains a major vaccine challenge. Most cross-conserved protein determinants are ...The elicitation of broadly neutralizing antibodies (bNAbs) against the HIV-1 envelope glycoprotein (Env) trimer remains a major vaccine challenge. Most cross-conserved protein determinants are occluded by self-N-glycan shielding, limiting B cell recognition of the underlying polypeptide surface. The exceptions to the contiguous glycan shield include the conserved receptor CD4 binding site (CD4bs) and glycoprotein (gp)41 elements proximal to the furin cleavage site. Accordingly, we performed heterologous trimer-liposome prime:boosting in rabbits to drive B cells specific for cross-conserved sites. To preferentially expose the CD4bs to B cells, we eliminated proximal N-glycans while maintaining the native-like state of the cleavage-independent NFL trimers, followed by gradual N-glycan restoration coupled with heterologous boosting. This approach successfully elicited CD4bs-directed, cross-neutralizing Abs, including one targeting a unique glycan-protein epitope and a bNAb (87% breadth) directed to the gp120:gp41 interface, both resolved by high-resolution cryoelectron microscopy. This study provides proof-of-principle immunogenicity toward eliciting bNAbs by vaccination. | |||||||||||||||
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_20273.map.gz | 11.8 MB | EMDB map data format | |
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Header (meta data) | emd-20273-v30.xml emd-20273.xml | 21.3 KB 21.3 KB | Display Display | EMDB header |
Images | emd_20273.png | 54.2 KB | ||
Others | emd_20273_half_map_1.map.gz emd_20273_half_map_2.map.gz | 11.9 MB 11.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20273 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20273 | HTTPS FTP |
-Validation report
Summary document | emd_20273_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_20273_full_validation.pdf.gz | 77.5 KB | Display | |
Data in XML | emd_20273_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20273 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20273 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20273.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | negative-stain 3D reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half map 1
File | emd_20273_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_20273_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 Env BG505 NFL CC+ trimer in complex with rabbit antibody E7...
Entire | Name: HIV-1 Env BG505 NFL CC+ trimer in complex with rabbit antibody E70 fragment antigen binding |
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Components |
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-Supramolecule #1: HIV-1 Env BG505 NFL CC+ trimer in complex with rabbit antibody E7...
Supramolecule | Name: HIV-1 Env BG505 NFL CC+ trimer in complex with rabbit antibody E70 fragment antigen binding type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 570 KDa |
-Macromolecule #1: HIV-1 Env BG505 NFL CC+ trimer
Macromolecule | Name: HIV-1 Env BG505 NFL CC+ trimer / 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: MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK DAETTLFCAS DAKAYETEKH NVWATHACVP TDPNPQEIHL ENVTEEFNMW KNNMVEQMHT DIISLWDQSL KPCVKLTPLC VTLQCTNVTN NITDDMRGEL KNCSFNMTTE LRDKKQKVYS LFYRLDVVQI ...String: MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK DAETTLFCAS DAKAYETEKH NVWATHACVP TDPNPQEIHL ENVTEEFNMW KNNMVEQMHT DIISLWDQSL KPCVKLTPLC VTLQCTNVTN NITDDMRGEL KNCSFNMTTE LRDKKQKVYS LFYRLDVVQI NENQGNRSNN SNKEYRLINC NTSACTQACP KVSFEPIPIH YCAPAGFAIL KCKDKKFNGT GPCPSVSTVQ CTHGIKPVVS TQLLLNGSLA EEEVMIRSEN ITNNAKNILV QFNTPVQINC TRPNNYTRKS IRIGPGQAFY ATGDIIGDIR QAHCNVSKAT WNETLGKVVK QLRKHFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQCMYAPP IQGVIRCVSN ITGLILTRDG GSTNSTTETF RPGGGDMRDN WRSELYKYKV VKIEPLGVAP TRAKRRVVGG GGGSGGGGSA VGIGAVRRGF LGAAGSTMGA ASMTLTVQAR NLLSGIVQQQ SNLLRAPEAQ QHLLKLTVWG IKQLQARVLA VERYLRDQQL LGIWGCSGKL ICTTNVPWNS SWSNRNLSEI WDNMTWLQWD KEISNYTQII YGLLEESQNQ QEKNEQDLLA LDGGGGSHHH HHHHH |
-Macromolecule #2: Rabbit antibody E70 fragment antigen binding heavy chain
Macromolecule | Name: Rabbit antibody E70 fragment antigen binding heavy chain type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QSLEESGGGL VKPGGTLTLT CKASGIDFTS GYDMCWVRQA PGKGLEWVAC IYLGDGNTYY ASWAKGQFTI SKTSSTTVTL QMTSLTAADT ATYFCARFAG YRYSVWSYPD LWGPGTLVTV SSGQPKAPSV FPLAPCCGDT PSSTVTLGCL VKGYLPEPVT VTWNSGTLTN ...String: QSLEESGGGL VKPGGTLTLT CKASGIDFTS GYDMCWVRQA PGKGLEWVAC IYLGDGNTYY ASWAKGQFTI SKTSSTTVTL QMTSLTAADT ATYFCARFAG YRYSVWSYPD LWGPGTLVTV SSGQPKAPSV FPLAPCCGDT PSSTVTLGCL VKGYLPEPVT VTWNSGTLTN GVRTFPSVRQ SSGLYSLSSV VSVTSSSQPV TCNVAHPATN TKVDKTVAPS TCSK |
-Macromolecule #3: Rabbit antibody E70 fragment antigen binding kappa chain
Macromolecule | Name: Rabbit antibody E70 fragment antigen binding kappa chain type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIVMTQTPAS VEADVGGTVT IKCQASQRIV NLVAWYQHKP GQPPKLLIIG ASDLASGVPS RFSGSGYGTE FTLTISDLEC ADAATYFCQS AYNGDGDNAF GGGTEVVVKG DPVAPSVLIF PPAADQVATG TVTIVCVANK YFPDVTVTWE VDGTTQTTGI ENSKTPQNSA ...String: DIVMTQTPAS VEADVGGTVT IKCQASQRIV NLVAWYQHKP GQPPKLLIIG ASDLASGVPS RFSGSGYGTE FTLTISDLEC ADAATYFCQS AYNGDGDNAF GGGTEVVVKG DPVAPSVLIF PPAADQVATG TVTIVCVANK YFPDVTVTWE VDGTTQTTGI ENSKTPQNSA DCTYNLSSTL TLTSTQYNSH KEYTCKVTQG TTSVVQSFNR GDC |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL | ||||||
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Buffer | pH: 7.4 Component:
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Staining | Type: NEGATIVE / Material: uranyl formate Details: Grids were negatively stained with 2% (w/v) uranyl formate for 50 s | ||||||
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / 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 / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |