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- EMDB-23153: Cryo-electron microscopy local refinement of antibody DH898.1 Fab... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23153 | |||||||||
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Title | Cryo-electron microscopy local refinement of antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848 10.17 SOSIP trimer | |||||||||
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Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.0 Å | |||||||||
![]() | Edwards RJ / Acharya P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler ...Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler Evangelous / Bhavna Hora / Madison Berry / A Yousef Abuahmad / Jordan Sprenz / Margaret Deyton / Victoria Stalls / Megan Kopp / Allen L Hsu / Mario J Borgnia / Guillaume B E Stewart-Jones / Matthew S Lee / Naomi Bronkema / M Anthony Moody / Kevin Wiehe / Todd Bradley / S Munir Alam / Robert J Parks / Andrew Foulger / Thomas Oguin / Gregory D Sempowski / Mattia Bonsignori / Celia C LaBranche / David C Montefiori / Michael Seaman / Sampa Santra / John Perfect / Joseph R Francica / Geoffrey M Lynn / Baptiste Aussedat / William E Walkowicz / Richard Laga / Garnett Kelsoe / Kevin O Saunders / Daniela Fera / Peter D Kwong / Robert A Seder / Alberto Bartesaghi / George M Shaw / Priyamvada Acharya / Barton F Haynes / ![]() ![]() Abstract: Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) ...Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (V) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without V-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgMIgDCD27, thus suggesting that they originated from a pool of antigen-experienced IgM or marginal zone B cells. #1: ![]() Title: Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques Authors: Williams WB / Meyerhoff RR / Edwards RJ / Li H / Nicely NI / Henderson R / Zhou Y / Janowska K / Mansouri K / Manne K / Stalls V / Hsu AL / Borgnia MJ / Stewart-Jones G / Lee MS / Bronkema N ...Authors: Williams WB / Meyerhoff RR / Edwards RJ / Li H / Nicely NI / Henderson R / Zhou Y / Janowska K / Mansouri K / Manne K / Stalls V / Hsu AL / Borgnia MJ / Stewart-Jones G / Lee MS / Bronkema N / Perfect J / Moody MA / Wiehe K / Bradley T / Kepler TB / Alam SM / Foulger A / Bonsignori M / LaBranche CC / Montefiori DC / Seaman M / Santra S / Francica JR / Lynn GM / Aussedat B / Walkowicz WE / Laga R / Kelso G / Saunders KO / Fera D / Kwong PD / Seder RA / Bartesaghi A / Shaw GM / Acharya P / Haynes BF | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31 KB 31 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.2 KB | Display | ![]() |
Images | ![]() | 159.5 KB | ||
Masks | ![]() ![]() | 125 MB 125 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() | 1.2 MB 61.1 MB 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 548.3 KB | Display | ![]() |
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Full document | ![]() | 547.9 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vtuC ![]() 6xrjC ![]() 7l02C ![]() 7l06C ![]() 7l09C ![]() 7l6mC ![]() 7l6oC ![]() 7lu9C ![]() 7luaC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.0665 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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-Mask #2
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-Additional map: #2
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-Additional map: #1
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-Half map: #2
File | emd_23153_half_map_1.map | ||||||||||||
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-Half map: #1
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Density Histograms |
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Sample components
-Entire : Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of ...
Entire | Name: Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer |
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Components |
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-Supramolecule #1: Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of ...
Supramolecule | Name: Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Molecular weight | Theoretical: 304 KDa |
-Supramolecule #2: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
Supramolecule | Name: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 210 KDa |
-Supramolecule #3: Antibody DH898.1 Fragment antigen binding (Fab) dimer
Supramolecule | Name: Antibody DH898.1 Fragment antigen binding (Fab) dimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: all / Details: Composed of two heavy chains and two light chains |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 94 KDa |
-Macromolecule #1: DH898.1 Fab heavy chain
Macromolecule | Name: DH898.1 Fab heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: QDLLLQSGAE VREPGASVTV SCQASNYTFP DYYIHWVRLV PGQGLEWLGE MKPKVGVTNV SKKIRDRLFM TADTSTDTAY MVLSALTPGD TAIYYCTRLE PDFLSGWAHW GKGVLVTVSP ASTKGPSVFP LAPSSRSTSE STAALGCLVK DYFPEPVTVS WNSGSLTSGV ...String: QDLLLQSGAE VREPGASVTV SCQASNYTFP DYYIHWVRLV PGQGLEWLGE MKPKVGVTNV SKKIRDRLFM TADTSTDTAY MVLSALTPGD TAIYYCTRLE PDFLSGWAHW GKGVLVTVSP ASTKGPSVFP LAPSSRSTSE STAALGCLVK DYFPEPVTVS WNSGSLTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YVCNVNHKPS NTKVDKRVE |
-Macromolecule #2: DH898.1 Fab light chain
Macromolecule | Name: DH898.1 Fab light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: EIVMTQTPLS LSVTPGEPAS LSCRSSASLL HGNGNTYLHW YLRKAGQSPQ LLIFGGSKRV PGISDRFIGS GAGTNFTLKI SSVEADDVGF YYCAQGVAFP WTFGQGTKVE IKRAVAAPSV FIFPPSEDQV KSGTVSVVCL LNNFYPREAS VKWKVDGVLK TGNSQESVTE ...String: EIVMTQTPLS LSVTPGEPAS LSCRSSASLL HGNGNTYLHW YLRKAGQSPQ LLIFGGSKRV PGISDRFIGS GAGTNFTLKI SSVEADDVGF YYCAQGVAFP WTFGQGTKVE IKRAVAAPSV FIFPPSEDQV KSGTVSVVCL LNNFYPREAS VKWKVDGVLK TGNSQESVTE QDSKDNTYSL SSTLTLSNTD YQSHNVYACE VTHQGLSSPV TKSFNRGE |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 12.0 nm | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP Details: 2.5 microliters of sample applied to grid and incubated for 30 seconds in chamber, blotted for 2.5 seconds, and plunge frozen in liquid ethane. | |||||||||
Details | For the DH898.1-bound complex, purified HIV-1 Env was mixed with 6-fold molar excess of recombinantly expressed and purified DH898.1 Fab to obtain a final Env concentration of 1.5 mg/ml, and incubated for 2 hours at room temperature. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 3230 / Average exposure time: 4.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |