PDBsum entry 6ozc

Viral protein

PDB id: 6ozc

Contents

Protein chains

435 a.a.

120 a.a.

(+ 0 more) 105 a.a.

(+ 0 more) 122 a.a.

Ligands

NAG-NAG-BMA-MAN-MAN-MAN ×3

NAG-NAG-BMA-MAN-MAN ×6

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN ×6

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN ×3

NAG-NAG-BMA-MAN-MAN-MAN-MAN ×3

NAG-NAG ×9

NAG ×21

PDB id:

6ozc

Name:

Viral protein

Title:

Bg505 sosip.664 with 2g12 fab2

Structure:

Envelope glycoprotein gp160. Chain: a, e, f. Synonym: env polyprotein. Engineered: yes. Envelope glycoprotein gp41. Chain: b, g, i. Engineered: yes. 2g12 fab light chain. Chain: l, d, q, m, r, n.

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Gene: env. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293f. Homo sapiens. Human. Organism_taxid: 9606.

Authors:

C.A.Cottrell,A.B.Ward

Key ref:

G.E.Seabright et al. (2020). Networks of HIV-1 Envelope Glycans Maintain Antibody Epitopes in the Face of Glycan Additions and Deletions. Structure, 28, 897. PubMed id: 32433992 DOI: 10.1016/j.str.2020.04.022

Date:

15-May-19 Release date: 20-May-20

Protein chains

Q2N0S6  (Q2N0S6_HV1) -  Envelope glycoprotein gp160 from Human immunodeficiency virus type 1

Seq: 860 a.a.

Struc: 435 a.a.*

Protein chains

Q2N0S6  (Q2N0S6_HV1) -  Envelope glycoprotein gp160 from Human immunodeficiency virus type 1

Seq: 860 a.a.

Struc: 120 a.a.*

Protein chains

No UniProt id for this chain

Struc: 105 a.a.

Protein chains

No UniProt id for this chain

Struc: 122 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1016/j.str.2020.04.022

Structure 28:897 (2020)

PubMed id: 32433992

Networks of HIV-1 Envelope Glycans Maintain Antibody Epitopes in the Face of Glycan Additions and Deletions.

G.E.Seabright, C.A.Cottrell, M.J.van Gils, A.D'addabbo, D.J.Harvey, A.J.Behrens, J.D.Allen, Y.Watanabe, N.Scaringi, T.M.Polveroni, A.Maker, S.Vasiljevic, N.de Val, R.W.Sanders, A.B.Ward, M.Crispin.

ABSTRACT

Numerous broadly neutralizing antibodies (bnAbs) have been identified that target the glycans of the HIV-1 envelope spike. Neutralization breadth is notable given that glycan processing can be substantially influenced by the presence or absence of neighboring glycans. Here, using a stabilized recombinant envelope trimer, we investigate the degree to which mutations in the glycan network surrounding an epitope impact the fine glycan processing of antibody targets. Using cryo-electron microscopy and site-specific glycan analysis, we reveal the importance of glycans in the formation of the 2G12 bnAb epitope and show that the epitope is only subtly impacted by variations in the glycan network. In contrast, we show that the PG9 and PG16 glycan-based epitopes at the trimer apex are dependent on the presence of the highly conserved surrounding glycans. Glycan networks underpin the conservation of bnAb epitopes and are an important parameter in immunogen design.