ISDA

Deposition Date 2020-12-11

Release Date 2020-12-30

Last Version Date 2024-11-13

Entry Detail

PDB ID:

7L09

Keywords:

VIRAL PROTEIN/IMMUNE SYSTEM

Title:

Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound domain-swapped antibody 2G12 from masked 3D refinement

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)
Homo sapiens (Taxon ID: 9606)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.10 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Gene (Uniprot):S
Chain IDs:A, B, C
Chain Length:1121
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF16451, PF09408, PF19209, PF01601

Polymer Type:polypeptide(L)
Molecule:2G12 heavy chain
Chain IDs:D (auth: H), G (auth: M)
Chain Length:226
Number of Molecules:2
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:2G12 light chain
Chain IDs:E (auth: K), F (auth: L)
Chain Length:213
Number of Molecules:2
Biological Source:Homo sapiens

Ligand Molecules

NAG

Primary Citation

Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.

Williams, W.B, Meyerhoff, R.R, Edwards, R.J, Li, H, Manne, K, Nicely, N.I, Henderson, R, Zhou, Y, Janowska, K, Mansouri, K, Gobeil, S, Evangelous, T, Hora, B, Berry, M, Abuahmad, A.Y, Sprenz, J, Deyton, M, Stalls, V, Kopp, M, Hsu, A.L, Borgnia, M.J, Stewart-Jones, G.B.E, Lee, M.S, Bronkema, N, Moody, M.A, Wiehe, K, Bradley, T, Alam, S.M, Parks, R.J, Foulger, A, Oguin, T, Sempowski, G.D, Bonsignori, M, LaBranche, C.C, Montefiori, D.C, Seaman, M, Santra, S, Perfect, J, Francica, J.R, Lynn, G.M, Aussedat, B, Walkowicz, W.E, Laga, R, Kelsoe, G, Saunders, K.O, Fera, D, Kwong, P.D, Seder, R.A, Bartesaghi, A, Shaw, G.M, Acharya, P, Haynes, B.F, Acharya, P, Williams, W, Henderson, R, Janowska, K, Manne, K, Parks, R, Deyton, M, Sprenz, J, Stalls, V, Kopp, M, Mansouri, K, Edwards, R.J, Meyerhoff, R.R, Oguin, T, Sempowski, G, Saunders, K, Haynes, B.F.Show

Cell 184 2955 ? (2021)

PMID: 34019795 DOI: 10.1016/j.cell.2021.04.042

Abstact

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 (VH) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without VH-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 IgM+IgD+CD27+, thus suggesting that they originated from a pool of antigen-experienced IgM+ or marginal zone B cells.

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Primary Citation of related structures