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Yorodumi- EMDB-7884: BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precur... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7884 | ||||||||||||
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Title | BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP1 fragment antigen binding and base-binding RM20A3 fragment antigen binding | ||||||||||||
Map data | Sharpened map | ||||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) / Macaca mulatta (Rhesus monkey) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.71 Å | ||||||||||||
Authors | Torres JL / Ozorowski G / Steichen JM / Schief WR / Ward AB | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Science / Year: 2019 Title: A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses. Authors: Jon M Steichen / Ying-Cing Lin / Colin Havenar-Daughton / Simone Pecetta / Gabriel Ozorowski / Jordan R Willis / Laura Toy / Devin Sok / Alessia Liguori / Sven Kratochvil / Jonathan L Torres ...Authors: Jon M Steichen / Ying-Cing Lin / Colin Havenar-Daughton / Simone Pecetta / Gabriel Ozorowski / Jordan R Willis / Laura Toy / Devin Sok / Alessia Liguori / Sven Kratochvil / Jonathan L Torres / Oleksandr Kalyuzhniy / Eleonora Melzi / Daniel W Kulp / Sebastian Raemisch / Xiaozhen Hu / Steffen M Bernard / Erik Georgeson / Nicole Phelps / Yumiko Adachi / Michael Kubitz / Elise Landais / Jeffrey Umotoy / Amanda Robinson / Bryan Briney / Ian A Wilson / Dennis R Burton / Andrew B Ward / Shane Crotty / Facundo D Batista / William R Schief / Abstract: Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for ...Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity-determining region 3 (HCDR3) is a major barrier. Exploiting ultradeep human antibody sequencing data, we identified a diverse set of potential antibody precursors for a bnAb with dominant HCDR3 contacts. We then developed HIV envelope trimer-based immunogens that primed responses from rare bnAb-precursor B cells in a mouse model and bound a range of potential bnAb-precursor human naïve B cells in ex vivo screens. Our repertoire-guided germline-targeting approach provides a framework for priming the induction of many HIV bnAbs and could be applied to most HCDR3-dominant antibodies from other pathogens. | ||||||||||||
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_7884.map.gz | 117 MB | EMDB map data format | |
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Header (meta data) | emd-7884-v30.xml emd-7884.xml | 27.1 KB 27.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7884_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_7884.png | 50 KB | ||
Masks | emd_7884_msk_1.map | 125 MB | Mask map | |
Others | emd_7884_half_map_1.map.gz emd_7884_half_map_2.map.gz | 98.4 MB 98.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7884 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7884 | HTTPS FTP |
-Validation report
Summary document | emd_7884_validation.pdf.gz | 536.1 KB | Display | EMDB validaton report |
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Full document | emd_7884_full_validation.pdf.gz | 535.7 KB | Display | |
Data in XML | emd_7884_validation.xml.gz | 16.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7884 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7884 | HTTPS FTP |
-Related structure data
Related structure data | 6nf5MC 7875C 7876C 7885C 6dfgC 6dfhC 6nfcC 6oc7C 7886 C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7884.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 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_7884_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_7884_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_7884_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precur...
Entire | Name: BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP1 fragment antigen binding and base-binding RM20A3 fragment antigen binding |
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Components |
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-Supramolecule #1: BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precur...
Supramolecule | Name: BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP1 fragment antigen binding and base-binding RM20A3 fragment antigen binding type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 720 KDa |
-Supramolecule #2: SOSIP trimer
Supramolecule | Name: SOSIP trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293F |
-Supramolecule #3: HMP1 fragment antigen binding
Supramolecule | Name: HMP1 fragment antigen binding / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293F |
-Supramolecule #4: RM20A3 fragment antigen binding
Supramolecule | Name: RM20A3 fragment antigen binding / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5 |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293F |
-Macromolecule #1: BG505 MD64 N332-GT5 SOSIP
Macromolecule | Name: BG505 MD64 N332-GT5 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: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPCV KLTPLCVTLQ CTNYAPKLRS MMRGEIKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE YRLINCNTSA ...String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPCV KLTPLCVTLQ CTNYAPKLRS MMRGEIKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE YRLINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV IIRSENITNN AKNILVQLNT PVQINCTRPS NNTVKSIRIG PGQAFYYFGD VLGHVRMAHC NISKATWNET LGKVVKQLRK HFGNNTIIRF AQSSGGDLEV TTHSFNCGGE FFYCNTSGLF NSTWISNTSV QGSNSTGSND SLILPCWIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRDNWRSE LYKYKVVKIE PLGVAPTRCK RRVVGRRRRR RAVGIGAVSL GFLGAAGSTM GAASMTLTVQ ARNLLSGIVQ QQSNLLRAPE PQQHLLKDTH WGIKQLQARV LAVEHYLRDQ QLLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDGTKHHH HHH |
-Macromolecule #2: BG18-like precursor HMP1 fragment antigen binding light chain
Macromolecule | Name: BG18-like precursor HMP1 fragment antigen binding light 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: SYELTQPPSV SVSPGQTARI TCSGDALPKQ YAYWYQQKPG QAPVLVIYKD SERPSGIPER FSGSSSGTTV TLTISGVQAE DEADYYCQSA DSSGEVFGGG TKLTVL |
-Macromolecule #3: BG18-like precursor HMP1 fragment antigen binding heavy chain
Macromolecule | Name: BG18-like precursor HMP1 fragment antigen binding heavy 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: QVQLQESGPG LVKPSQTLSL TCTVSGGSIS SGSYYWSWIR QPAGKGLEWI GRIYTSGSTN YNPSLKSRVT ISVDTSKNQF SLKLSSVTAA DTAVYYCARE GFTIFGVVTF SEGYYYGMDV WGKGTTVTVS S |
-Macromolecule #4: RM20A3 fragment antigen binding light chain
Macromolecule | Name: RM20A3 fragment antigen binding light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ALTQPPSVSG SPGQSVTISC TGTSSDIGSY NYVSWYQQHP GKAPKLMIYD VTQRPSGVSD RFSGSKSGNT ASLTISGLQA DDEADYYCSA YAGRQTFYIF GGGTRLTVLG QPKASPTVTL FPPSSEEL |
-Macromolecule #5: RM20A3 fragment antigen binding heavy chain
Macromolecule | Name: RM20A3 fragment antigen binding heavy chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVETGGG LVQPGGSLKL SCRASGYTFS SFAMSWVRQA PGKGLEWVSL INDRGGLTFY VDSVKGRFTI SRDNSKNTLS LQMHSLRDGD TAVYYCATGG MSSALQSSKY YFDFWGQGAL VTVSS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.9 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: Detergent (DDM) added immediately prior to grid preparation | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Details: Gatan Model 950 Advanced Plasma System | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: 6 seconds blotting time. | ||||||||||||
Details | SEC purified complex |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 1796 / Average exposure time: 11.75 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |