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Genome organization of <t>an</t> <t>HIV-1</t> clone used in this study. Genomes of NL-gtu+Y3/NL-gtu+Y3ad are schematically shown. White and gray areas represent the sequences from HIV-1(NL4-3) and SIVgsn166 (GenBank: AF468659 ), respectively. Green boxes show the env sequence from a clinical isolate (GenBank: LC816726 ). The unique restriction enzyme sites of the genomes used to generate HIV-1 clones are indicated.
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Genome organization of <t>an</t> <t>HIV-1</t> clone used in this study. Genomes of NL-gtu+Y3/NL-gtu+Y3ad are schematically shown. White and gray areas represent the sequences from HIV-1(NL4-3) and SIVgsn166 (GenBank: AF468659 ), respectively. Green boxes show the env sequence from a clinical isolate (GenBank: LC816726 ). The unique restriction enzyme sites of the genomes used to generate HIV-1 clones are indicated.
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Genome organization of <t>an</t> <t>HIV-1</t> clone used in this study. Genomes of NL-gtu+Y3/NL-gtu+Y3ad are schematically shown. White and gray areas represent the sequences from HIV-1(NL4-3) and SIVgsn166 (GenBank: AF468659 ), respectively. Green boxes show the env sequence from a clinical isolate (GenBank: LC816726 ). The unique restriction enzyme sites of the genomes used to generate HIV-1 clones are indicated.
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Genome organization of <t>an</t> <t>HIV-1</t> clone used in this study. Genomes of NL-gtu+Y3/NL-gtu+Y3ad are schematically shown. White and gray areas represent the sequences from HIV-1(NL4-3) and SIVgsn166 (GenBank: AF468659 ), respectively. Green boxes show the env sequence from a clinical isolate (GenBank: LC816726 ). The unique restriction enzyme sites of the genomes used to generate HIV-1 clones are indicated.
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Genome organization of <t>an</t> <t>HIV-1</t> clone used in this study. Genomes of NL-gtu+Y3/NL-gtu+Y3ad are schematically shown. White and gray areas represent the sequences from HIV-1(NL4-3) and SIVgsn166 (GenBank: AF468659 ), respectively. Green boxes show the env sequence from a clinical isolate (GenBank: LC816726 ). The unique restriction enzyme sites of the genomes used to generate HIV-1 clones are indicated.
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Genome organization of <t>an</t> <t>HIV-1</t> clone used in this study. Genomes of NL-gtu+Y3/NL-gtu+Y3ad are schematically shown. White and gray areas represent the sequences from HIV-1(NL4-3) and SIVgsn166 (GenBank: AF468659 ), respectively. Green boxes show the env sequence from a clinical isolate (GenBank: LC816726 ). The unique restriction enzyme sites of the genomes used to generate HIV-1 clones are indicated.
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Genome organization of <t>an</t> <t>HIV-1</t> clone used in this study. Genomes of NL-gtu+Y3/NL-gtu+Y3ad are schematically shown. White and gray areas represent the sequences from HIV-1(NL4-3) and SIVgsn166 (GenBank: AF468659 ), respectively. Green boxes show the env sequence from a clinical isolate (GenBank: LC816726 ). The unique restriction enzyme sites of the genomes used to generate HIV-1 clones are indicated.
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Genome organization of <t>an</t> <t>HIV-1</t> clone used in this study. Genomes of NL-gtu+Y3/NL-gtu+Y3ad are schematically shown. White and gray areas represent the sequences from HIV-1(NL4-3) and SIVgsn166 (GenBank: AF468659 ), respectively. Green boxes show the env sequence from a clinical isolate (GenBank: LC816726 ). The unique restriction enzyme sites of the genomes used to generate HIV-1 clones are indicated.
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Genome organization of an HIV-1 clone used in this study. Genomes of NL-gtu+Y3/NL-gtu+Y3ad are schematically shown. White and gray areas represent the sequences from HIV-1(NL4-3) and SIVgsn166 (GenBank: AF468659 ), respectively. Green boxes show the env sequence from a clinical isolate (GenBank: LC816726 ). The unique restriction enzyme sites of the genomes used to generate HIV-1 clones are indicated.

Journal: Frontiers in Microbiology

Article Title: Natural variations at the E433 site in Env-gp120 β20-β21 cooperate with V2 and gp41 mutations to modulate HIV-1 infectivity

doi: 10.3389/fmicb.2026.1877899

Figure Lengend Snippet: Genome organization of an HIV-1 clone used in this study. Genomes of NL-gtu+Y3/NL-gtu+Y3ad are schematically shown. White and gray areas represent the sequences from HIV-1(NL4-3) and SIVgsn166 (GenBank: AF468659 ), respectively. Green boxes show the env sequence from a clinical isolate (GenBank: LC816726 ). The unique restriction enzyme sites of the genomes used to generate HIV-1 clones are indicated.

Article Snippet: For neutralization assays, virus stocks were pretreated with sCD4 (catalog no. CYT-304; ProSpec-Tany Technogene Ltd.) or various anti-HIV-1 gp120 antibodies for 1 hr at 37 °C before inoculation.

Techniques: Sequencing, Clone Assay

Effect of amino acid mutations at the E433 residue on virus infectivity. (A) Sequence analysis. The web logos of the sequences around the β20ß21 strands of subtype CRF08_BC (41 sequences) and B (2,334 sequences) were generated using the HIV-1 sequence database ( https://www.hiv.lanl.gov/content/index ). The HXB2 numbering of Env sequence is presented at the bottom of the web logos. The location of the β20-β21 strands is indicated. Orange boxes show the Y3-E433 site. (B) Virus infectivity. Infectivity of Y3, Y3ad-2, and Y3ad2-derived clones was analyzed as described in the legend to . Mean values ± SE from four independent experiments are shown. See for the mean values ± SE and p -values by the Welch's t -test.

Journal: Frontiers in Microbiology

Article Title: Natural variations at the E433 site in Env-gp120 β20-β21 cooperate with V2 and gp41 mutations to modulate HIV-1 infectivity

doi: 10.3389/fmicb.2026.1877899

Figure Lengend Snippet: Effect of amino acid mutations at the E433 residue on virus infectivity. (A) Sequence analysis. The web logos of the sequences around the β20ß21 strands of subtype CRF08_BC (41 sequences) and B (2,334 sequences) were generated using the HIV-1 sequence database ( https://www.hiv.lanl.gov/content/index ). The HXB2 numbering of Env sequence is presented at the bottom of the web logos. The location of the β20-β21 strands is indicated. Orange boxes show the Y3-E433 site. (B) Virus infectivity. Infectivity of Y3, Y3ad-2, and Y3ad2-derived clones was analyzed as described in the legend to . Mean values ± SE from four independent experiments are shown. See for the mean values ± SE and p -values by the Welch's t -test.

Article Snippet: For neutralization assays, virus stocks were pretreated with sCD4 (catalog no. CYT-304; ProSpec-Tany Technogene Ltd.) or various anti-HIV-1 gp120 antibodies for 1 hr at 37 °C before inoculation.

Techniques: Residue, Virus, Infection, Sequencing, Analysis, Generated, Derivative Assay, Clone Assay

The location of adaptive mutation site. The surface representation of the gp120 trimer is illustrated in light gray. Left; Adaptive mutation sites found in Y3ad-2 (D166, N195, and E433) are indicated. Right; the surface of residues D166 (red) and K168 (blue) is highlighted to illustrate their spatial arrangement within the V1/V2 loop region. These residues are positioned at the trimer apex and form a cluster that may influence inter-subunit interactions and structural stability of the envelope glycoprotein.

Journal: Frontiers in Microbiology

Article Title: Natural variations at the E433 site in Env-gp120 β20-β21 cooperate with V2 and gp41 mutations to modulate HIV-1 infectivity

doi: 10.3389/fmicb.2026.1877899

Figure Lengend Snippet: The location of adaptive mutation site. The surface representation of the gp120 trimer is illustrated in light gray. Left; Adaptive mutation sites found in Y3ad-2 (D166, N195, and E433) are indicated. Right; the surface of residues D166 (red) and K168 (blue) is highlighted to illustrate their spatial arrangement within the V1/V2 loop region. These residues are positioned at the trimer apex and form a cluster that may influence inter-subunit interactions and structural stability of the envelope glycoprotein.

Article Snippet: For neutralization assays, virus stocks were pretreated with sCD4 (catalog no. CYT-304; ProSpec-Tany Technogene Ltd.) or various anti-HIV-1 gp120 antibodies for 1 hr at 37 °C before inoculation.

Techniques: Mutagenesis, Stability

A molecular dynamics simulation analysis of HIV-1 gp120-CD4 complexes. Structural models of gp120-CD4 complexes at 100 ns (left) and corresponding close-up views of gp120 around residue 433 (right). Left: HIV-1 gp120 is shown in blue and CD4 in orange. The V1/V2 loop region is indicated by a red dashed circle. N-linked glycans are shown as stick representations (cyan). Right: Views are from the gp120 regions indicated by red boxes toward the gp120 surface surrounding residue 433. E433 or E433R is shown as a stick representation (white) and highlighted by a yellow dashed circle. Molecular surfaces are colored according to electrostatic potential, with red indicating negative charge and blue indicating positive charge. For easy comparison, the α1 helix and β20-β21 strands are indicated.

Journal: Frontiers in Microbiology

Article Title: Natural variations at the E433 site in Env-gp120 β20-β21 cooperate with V2 and gp41 mutations to modulate HIV-1 infectivity

doi: 10.3389/fmicb.2026.1877899

Figure Lengend Snippet: A molecular dynamics simulation analysis of HIV-1 gp120-CD4 complexes. Structural models of gp120-CD4 complexes at 100 ns (left) and corresponding close-up views of gp120 around residue 433 (right). Left: HIV-1 gp120 is shown in blue and CD4 in orange. The V1/V2 loop region is indicated by a red dashed circle. N-linked glycans are shown as stick representations (cyan). Right: Views are from the gp120 regions indicated by red boxes toward the gp120 surface surrounding residue 433. E433 or E433R is shown as a stick representation (white) and highlighted by a yellow dashed circle. Molecular surfaces are colored according to electrostatic potential, with red indicating negative charge and blue indicating positive charge. For easy comparison, the α1 helix and β20-β21 strands are indicated.

Article Snippet: For neutralization assays, virus stocks were pretreated with sCD4 (catalog no. CYT-304; ProSpec-Tany Technogene Ltd.) or various anti-HIV-1 gp120 antibodies for 1 hr at 37 °C before inoculation.

Techniques: Analysis, Residue, Comparison