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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23518 | |||||||||
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Title | Cryo-EM map of DH851.3 bound to HIV-1 CH505 Env | |||||||||
![]() | CryoEM map of DH851.3 bound to HIV-1 CH505 Env | |||||||||
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Function / homology | ![]() virus-mediated perturbation of host defense response => GO:0019049 / : / 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 / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane ...virus-mediated perturbation of host defense response => GO:0019049 / : / 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 / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.6 Å | |||||||||
![]() | Edwards RJ / Manne K / 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: Acharya P / Williams W / Henderson R / Janowska K / Manne K / Parks R / Deyton M / Sprenz J / Stalls V / Kopp M / Mansouri K / Edwards RJ / Meyerhoff RR / Oguin T / Sempowski G / Saunders K / 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 | ![]() | 25.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.4 KB 26.4 KB | Display Display | ![]() |
Images | ![]() | 70.9 KB | ||
Others | ![]() ![]() | 200.4 MB 200.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 805.3 KB | Display | ![]() |
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Full document | ![]() | 804.9 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lu9MC ![]() 6vtuC ![]() 6xrjC ![]() 7l02C ![]() 7l06C ![]() 7l09C ![]() 7l6mC ![]() 7l6oC ![]() 7luaC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of DH851.3 bound to HIV-1 CH505 Env | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Half map: CryoEM half-map B of DH851.3 bound to HIV-1 CH505 Env
File | emd_23518_half_map_1.map | ||||||||||||
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Annotation | CryoEM half-map B of DH851.3 bound to HIV-1 CH505 Env | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM half-map A of DH851.3 bound to HIV-1 CH505 Env
File | emd_23518_half_map_2.map | ||||||||||||
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Annotation | CryoEM half-map A of DH851.3 bound to HIV-1 CH505 Env | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : DH851.3 bound to HIV-1 CH505 Env
Entire | Name: DH851.3 bound to HIV-1 CH505 Env |
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Components |
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-Supramolecule #1: DH851.3 bound to HIV-1 CH505 Env
Supramolecule | Name: DH851.3 bound to HIV-1 CH505 Env / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: DH851.3 light chain
Macromolecule | Name: DH851.3 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 22.127463 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN ...String: ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN NKYAASSYLS LTSDQWKSHK SYSCQVTHEG STVEKTVAPA EC |
-Macromolecule #2: DH851.3 heavy chain
Macromolecule | Name: DH851.3 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.451617 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS ...String: QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVEIKTCGG |
-Macromolecule #3: DH851.3 heavy chain
Macromolecule | Name: DH851.3 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.89093 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS ...String: QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVE |
-Macromolecule #4: DH851.3 light chain
Macromolecule | Name: DH851.3 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.824127 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN ...String: ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN NKYAASSYLS LTSDQWKSHK SYSCQVTHEG STVEKTVAP |
-Macromolecule #5: Envelope glycoprotein gp41
Macromolecule | Name: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.134512 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLKAIEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD |
-Macromolecule #6: Envelope glycoprotein gp120
Macromolecule | Name: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 51.898062 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNVWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS V ITQACPKV ...String: ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNVWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS V ITQACPKV SFDPIPIHYC APAGYAILKC NNKTFTGTGP CNNVSTVQCT HGIKPVVSTQ LLLNGSLAEG EIIIRSENIT NN VKTIIVH LNESVKIECT RPNNKTRTSI RIGPGQWFYA TGQVIGDIRE AYCNINESKW NETLQRVSKK LKEYFPHKNI TFQ PSSGGD LEITTHSFNC GGEFFYCNTS SLFNRTYMAN STDMANSTET NSTRTITIHC RIKQIINMWQ EVGRAMYAPP IAGN ITCIS NITGLLLTRD GGKNNTETFR PGGGNMKDNW RSELYKYKVV KIEPLGVAPT RCKRRV |
-Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 3 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: blot for 2.5 seconds before plunging. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 93.15 K / Max: 93.15 K |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 6058 / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Software - Name: cryoSPARC |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53398 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7lu9: |