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Yorodumi- EMDB-50020: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in com... -
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Open data
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Basic information
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| Title | HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody. | ||||||||||||||||||
Map data | Final map filtered with DeepEMhancer. Suitable for illustration purposes. | ||||||||||||||||||
Sample |
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Keywords | HIV-1 / envelope glycoprotein / gp140 / neutralizing antibody / VIRAL PROTEIN | ||||||||||||||||||
| Biological species | Homo sapiens (human) / ![]() Human immunodeficiency virus 1 | ||||||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||||||||||||||
Authors | Hope J / Alguel Y / Nans A / Cherepanov P | ||||||||||||||||||
| Funding support | United States, United Kingdom, 5 items
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Citation | Journal: To Be PublishedTitle: TITLE: Preservation of memory B cell homeostasis in an individual producing broadly neutralizing antibodies against HIV-1 Authors: Griffith S / Muir L / Suchanek O / Hope J / Pade C / Gibbons G / Tuong K / Fung A / Touizer E / Rees-Spear C / Nans A / Roustan C / Alguel Y / Fink D / Orkin C / Deayton J / Anderson J / ...Authors: Griffith S / Muir L / Suchanek O / Hope J / Pade C / Gibbons G / Tuong K / Fung A / Touizer E / Rees-Spear C / Nans A / Roustan C / Alguel Y / Fink D / Orkin C / Deayton J / Anderson J / Gupta RK / Doores KJ / Cherepanov P / McKnight A / Clatworthy M / McCoy LE | ||||||||||||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_50020.map.gz | 151.7 MB | EMDB map data format | |
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| Header (meta data) | emd-50020-v30.xml emd-50020.xml | 28.2 KB 28.2 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_50020_fsc.xml | 11.9 KB | Display | FSC data file |
| Images | emd_50020.png | 122.9 KB | ||
| Masks | emd_50020_msk_1.map emd_50020_msk_2.map | 178 MB 178 MB | Mask map | |
| Filedesc metadata | emd-50020.cif.gz | 7.9 KB | ||
| Others | emd_50020_additional_1.map.gz emd_50020_half_map_1.map.gz emd_50020_half_map_2.map.gz | 6 MB 165.4 MB 165.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50020 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50020 | HTTPS FTP |
-Related structure data
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Map
| File | Download / File: emd_50020.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Final map filtered with DeepEMhancer. Suitable for illustration purposes. | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_50020_msk_1.map | ||||||||||||
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| Density Histograms |
-Mask #2
| File | emd_50020_msk_2.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Additional map: Locally filtered sharpened map. Used for real-space refinement.
| File | emd_50020_additional_1.map | ||||||||||||
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| Annotation | Locally filtered sharpened map. Used for real-space refinement. | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Half-map A.
| File | emd_50020_half_map_1.map | ||||||||||||
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| Annotation | Half-map A. | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Half-map B.
| File | emd_50020_half_map_2.map | ||||||||||||
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| Annotation | Half-map B. | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
-Entire : HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in com...
| Entire | Name: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody |
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| Components |
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-Supramolecule #1: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in com...
| Supramolecule | Name: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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| Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Envelope glycoprotein gp41
| Macromolecule | Name: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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| Source (natural) | Organism: ![]() Human immunodeficiency virus 1 / Strain: BG505 SOSIP.664 |
| Molecular weight | Theoretical: 19.10359 KDa |
| Recombinant expression | Organism: Homo sapiens (human) |
| Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDGSGLND I FEAQKIEW HE |
-Macromolecule #2: Envelope glycoprotein gp120
| Macromolecule | Name: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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| Source (natural) | Organism: ![]() Human immunodeficiency virus 1 / Strain: BG505 SOSIP.664 |
| Molecular weight | Theoretical: 57.945977 KDa |
| Recombinant expression | Organism: Homo sapiens (human) |
| Sequence | String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK ...String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK VYSLFYRLDV VQINENQGNR SNNSNKEYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NG TGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAF YATGDI IGDIRQAHCN VSKATWNETL GKVVKQLRKH FGNNTIIRFA NSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWI SNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRD NWRS ELYKYKVVKI EPLGVAPTRC KRRVVGRRRR RR |
-Macromolecule #3: ELC07 heavy chain
| Macromolecule | Name: ELC07 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 28.586055 KDa |
| Recombinant expression | Organism: Homo sapiens (human) |
| Sequence | String: METDTLLLWV LLLWVPGSTG EVQLVQSGAE LKKAGSSVKL SCQAYGVAFS TYSFHWVRQA PGQGLEWLGG FIPLVGKPNY TNKFRGRLT ITADESARTT YMELRSLRSD DTAIYYCAGG GAYSSGGGRF HYFGMAVWGQ GSTVTVSSAS TKGPSVFPLA P SSKSTSGG ...String: METDTLLLWV LLLWVPGSTG EVQLVQSGAE LKKAGSSVKL SCQAYGVAFS TYSFHWVRQA PGQGLEWLGG FIPLVGKPNY TNKFRGRLT ITADESARTT YMELRSLRSD DTAIYYCAGG GAYSSGGGRF HYFGMAVWGQ GSTVTVSSAS TKGPSVFPLA P SSKSTSGG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TK VDKRVEP KSCGSGENLY FQSAGHHHHH H |
-Macromolecule #4: ELC07 light chain
| Macromolecule | Name: ELC07 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 25.599775 KDa |
| Recombinant expression | Organism: Homo sapiens (human) |
| Sequence | String: MTQTPASLLF LLLLWLPGAK CDIQLTQSPS TLSAPVGAGV TITCQASQSI SNGLAWYQQK PGRAPKMLIT EGSSLKSGVP DRFRGSGSG THFILTISDL QPDDSATYFC QQYNTFPWTF GRGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String: MTQTPASLLF LLLLWLPGAK CDIQLTQSPS TLSAPVGAGV TITCQASQSI SNGLAWYQQK PGRAPKMLIT EGSSLKSGVP DRFRGSGSG THFILTISDL QPDDSATYFC QQYNTFPWTF GRGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose
| Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 27 / 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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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 1 mg/mL | |||||||||
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| Buffer | pH: 7.5 Component:
Details: 150 mM NaCl, 50 mM Tris-HCl, pH 7.5 | |||||||||
| Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||
| Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 33.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.3 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Initial model |
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| Refinement | Protocol: RIGID BODY FIT | ||||||||||
| Output model | ![]() PDB-9evz: |
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About Yorodumi



Keywords
Homo sapiens (human)
Human immunodeficiency virus 1
Authors
United States,
United Kingdom, 5 items
Citation


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FIELD EMISSION GUN


