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Title | Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces. |
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Journal, issue, pages | Nat Commun, Vol. 12, Issue 1, Page 6470, Year 2021 |
Publish date | Nov 9, 2021 |
Authors | Myungjin Lee / Anita Changela / Jason Gorman / Reda Rawi / Tatsiana Bylund / Cara W Chao / Bob C Lin / Mark K Louder / Adam S Olia / Baoshan Zhang / Nicole A Doria-Rose / Susan Zolla-Pazner / Lawrence Shapiro / Gwo-Yu Chuang / Peter D Kwong / |
PubMed Abstract | Antibody-Framework-to-Antigen Distance (AFAD) - the distance between the body of an antibody and a protein antigen - is an important parameter governing antibody recognition. Here, we quantify AFAD ...Antibody-Framework-to-Antigen Distance (AFAD) - the distance between the body of an antibody and a protein antigen - is an important parameter governing antibody recognition. Here, we quantify AFAD for ~2,000 non-redundant antibody-protein-antigen complexes in the Protein Data Bank. AFADs showed a gaussian distribution with mean of 16.3 Å and standard deviation (σ) of 2.4 Å. Notably, antibody-antigen complexes with extended AFADs (>3σ) were exclusively human immunodeficiency virus-type 1 (HIV-1)-neutralizing antibodies. High correlation (R = 0.8110) was observed between AFADs and glycan coverage, as assessed by molecular dynamics simulations of the HIV-1-envelope trimer. Especially long AFADs were observed for antibodies targeting the glycosylated trimer apex, and we tested the impact of introducing an apex-glycan hole (N160K); the cryo-EM structure of the glycan hole-targeting HIV-1-neutralizing antibody 2909 in complex with an N160K-envelope trimer revealed a substantially shorter AFAD. Overall, extended AFADs exclusively recognized densely glycosylated surfaces, with the introduction of a glycan hole enabling closer recognition. |
External links | Nat Commun / PubMed:34753907 / PubMed Central |
Methods | EM (single particle) |
Resolution | 3.91 Å |
Structure data | EMDB-23589, PDB-7ly9: |
Chemicals | ChemComp-NAG: |
Source |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / CAP256 / V1V2 / V2-Apex / SOSIP / Vaccine / TYS / VIRAL PROTEIN-IMMUNE SYSTEM complex |