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Structure paper

TitleMapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates.
Journal, issue, pagesPLoS Pathog, Vol. 16, Issue 8, Page e1008753, Year 2020
Publish dateAug 31, 2020
AuthorsChristopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / Raj Patel / Justin Gross / Leigh M Sewall / Jeffrey Copps / Gabriel Ozorowski / Bartek Nogal / Devin Sok / Eva G Rakasz / Celia Labranche / Vladimir Vigdorovich / Scott Christley / Diane G Carnathan / D Noah Sather / David Montefiori / Guido Silvestri / Dennis R Burton / John P Moore / Ian A Wilson / Rogier W Sanders / Andrew B Ward / Marit J van Gils /
PubMed AbstractThe induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown ...The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.
External linksPLoS Pathog / PubMed:32866207 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.85 - 29.0 Å
Structure data

EMDB-21053:
RM19N Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-21055:
RM19J Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 15.0 Å

EMDB-21056:
RM19F Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 26.0 Å

EMDB-21057:
RM19T Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 27.0 Å

EMDB-21058:
RM19R Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 21.0 Å

EMDB-21059:
RM19S Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-21061:
RM19M Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 18.0 Å

EMDB-21062:
RM19A1 Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 22.0 Å

EMDB-21064:
RM19P Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 18.0 Å

EMDB-21065:
RM19O Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 29.0 Å

EMDB-21066:
RM19L Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 16.0 Å

EMDB-21075:
RM19B Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 15.0 Å

EMDB-21076:
RM19K Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 17.0 Å

EMDB-21077:
RM19B1 Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 27.0 Å

EMDB-21078:
RM19C Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 29.0 Å

EMDB-21079:
RM19C2 Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 27.0 Å

EMDB-21080:
RM19E Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 17.0 Å

EMDB-21081:
RM19G Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 21.0 Å

EMDB-21082:
RM19C3 Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 18.0 Å

EMDB-21083:
RM20A2 Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-21084:
RM20A3 Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 15.0 Å

EMDB-21085:
RM20B Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-21086:
RM20B1 Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 23.0 Å

EMDB-21087:
RM20C Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 15.0 Å

EMDB-21088:
RM20G Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 21.0 Å

EMDB-21089:
RM20J Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-21090:
RM20E1 Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 21.0 Å

EMDB-21091:
RM20F Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 15.0 Å

EMDB-21092:
RM20H Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 27.0 Å

EMDB-21093:
RM20E Fab in complex with BG505 SOSIPv5.2
Method: EM (single particle) / Resolution: 20.0 Å

21232

6vlr

EMDB-21232, PDB-6vlr:
BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab
Method: EM (single particle) / Resolution: 4.42 Å

21246

6vn0

EMDB-21246, PDB-6vn0:
BG505 SOSIP.v4.1 in complex with rhesus macaque Fab RM20F
Method: EM (single particle) / Resolution: 4.25 Å

21257

6vo1

EMDB-21257, PDB-6vo1:
BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20J
Method: EM (single particle) / Resolution: 3.88 Å

EMDB-21272:
Polyclonal Fabs from rhesus macaque rh2011 wk28 plasma in complex with HIV Env trimer BG505 SOSIP.v5.2
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-21273:
Polyclonal Fabs from rhesus macaque rh2011 wk28 plasma in complex with HIV Env trimer BG505 SOSIP.v5.2
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-21274:
Polyclonal Fabs from rhesus macaque rh2011 wk28 plasma in complex with HIV Env trimer BG505 SOSIP.v5.2
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-21275:
Polyclonal Fabs from rhesus macaque rh2011 wk28 plasma in complex with HIV Env trimer BG505 SOSIP.v5.2
Method: EM (single particle) / Resolution: 27.0 Å

EMDB-21276:
Polyclonal Fabs from rhesus macaque rh1987 wk28 plasma in complex with HIV Env trimer BG505 SOSIP.v5.2
Method: EM (single particle) / Resolution: 18.0 Å

EMDB-21277:
Polyclonal Fabs from rhesus macaque rh1987 wk28 plasma in complex with HIV Env trimer BG505 SOSIP.v5.2
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-21278:
Polyclonal Fabs from rhesus macaque rh1987 wk28 plasma in complex with HIV Env trimer BG505 SOSIP.v5.2
Method: EM (single particle) / Resolution: 15.2 Å

PDB-6vor:
Crystal structure of macaque anti-HIV-1 antibody RM20E1
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-6vos:
Crystal structure of macaque anti-HIV-1 antibody RM20J
Method: X-RAY DIFFRACTION / Resolution: 2.299 Å

PDB-6vsr:
Crystal structure of macaque anti-HIV-1 antibody RM20F
Method: X-RAY DIFFRACTION / Resolution: 2.176 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-GLY:
GLYCINE

ChemComp-HOH:
WATER

ChemComp-TAM:
TRIS(HYDROXYETHYL)AMINOMETHANE / pH buffer*YM

ChemComp-2PE:
NONAETHYLENE GLYCOL / precipitant*YM

ChemComp-P6G:
HEXAETHYLENE GLYCOL / precipitant*YM

ChemComp-PE8:
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL

ChemComp-SO4:
SULFATE ION

Source
  • macaca mulatta (Rhesus monkey)
  • human immunodeficiency virus 1
  • homo sapiens (human)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / antibody / Fab / vaccine / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex / Rhesus macaque / IMMUNE SYSTEM / non-human primates

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