ISDA

Deposition Date 2021-02-21

Release Date 2021-03-17

Last Version Date 2024-11-06

Entry Detail

PDB ID:

7LUA

Keywords:

VIRAL PROTEIN/IMMUNE SYSTEM

Title:

Cryo-EM structure of DH898.1 Fab-dimer bound near the CD4 binding site of HIV-1 Env CH848 SOSIP trimer

Biological Source:

Source Organism:

Human immunodeficiency virus 1 (Taxon ID: 11676)
Simian-Human immunodeficiency virus (Taxon ID: 57667)
Homo sapiens (Taxon ID: 9606)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

4.70 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CH848 SOSIP gp120
Gene (Uniprot):env
Chain IDs:A (auth: a), C (auth: c), E (auth: e)
Chain Length:466
Number of Molecules:3
Biological Source:Human immunodeficiency virus 1

UniProt ID:A0A1W6IPB2 Pfam ID:PF00516

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Env polyprotein
Chain IDs:B (auth: b), D (auth: d), F (auth: f)
Chain Length:146
Number of Molecules:3
Biological Source:Simian-Human immunodeficiency virus

UniProt ID:A0A6H1V945 Pfam ID:PF00517

Polymer Type:polypeptide(L)
Molecule:DH898.1 light chain
Chain IDs:G (auth: g), J (auth: j)
Chain Length:218
Number of Molecules:2
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:DH898.1 heavy chain
Chain IDs:H (auth: h), I (auth: i)
Chain Length:219
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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