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Structure paper

TitleHIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies.
Journal, issue, pagesCell Rep, Vol. 31, Issue 4, Page 107583, Year 2020
Publish dateApr 28, 2020
AuthorsKimmo Rantalainen / Zachary T Berndsen / Aleksandar Antanasijevic / Torben Schiffner / Xi Zhang / Wen-Hsin Lee / Jonathan L Torres / Lei Zhang / Adriana Irimia / Jeffrey Copps / Kenneth H Zhou / Young D Kwon / William H Law / Chaim A Schramm / Raffaello Verardi / Shelly J Krebs / Peter D Kwong / Nicole A Doria-Rose / Ian A Wilson / Michael B Zwick / John R Yates / William R Schief / Andrew B Ward /
PubMed AbstractStructural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the ...Structural and functional studies of HIV envelope glycoprotein (Env) as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the membrane-embedded hydrophobic regions. Here, we present approaches for incorporating full-length, wild-type HIV-1 Env, as well as C-terminally truncated and stabilized versions, into lipid assemblies, providing a modular platform for Env structural studies by single particle electron microscopy. We reconstitute a full-length Env clone into a nanodisc, complex it with a membrane-proximal external region (MPER) targeting antibody 10E8, and structurally define the full quaternary epitope of 10E8 consisting of lipid, MPER, and ectodomain contacts. By aligning this and other Env-MPER antibody complex reconstructions with the lipid bilayer, we observe evidence of Env tilting as part of the neutralization mechanism for MPER-targeting antibodies. We also adapt the platform toward vaccine design purposes by introducing stabilizing mutations that allow purification of unliganded Env with a peptidisc scaffold.
External linksCell Rep / PubMed:32348769 / PubMed Central
MethodsEM (single particle)
Resolution4.6 - 26.0 Å
Structure data

EMDB-21321:
Full-length HIV-1 Envelope glycoprotein clone PC64 in complex with PGT151 Fab and VRC42.01 Fab
Method: EM (single particle) / Resolution: 7.4 Å

EMDB-21322:
Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and VRC42.01 Fab
Method: EM (single particle) / Resolution: 7.2 Å

EMDB-21323:
Full-length HIV-1 Envelope glycoprotein clone PC64 in complex with PGT151 Fab and VRC42.N1 Fab
Method: EM (single particle) / Resolution: 8.6 Å

EMDB-21324:
Full-length HIV-1 Envelope glycoprotein clone PC64 in complex with PGT151 Fab and DH511.2 Fab
Method: EM (single particle) / Resolution: 7.6 Å

EMDB-21326:
Full-length HIV-1 Envelope glycoprotein clone PC64FL in complex with PGT151 Fab and VRC46.01 Fab
Method: EM (single particle) / Resolution: 9.0 Å

EMDB-21327:
Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and two copies of PGZL1 Fab
Method: EM (single particle) / Resolution: 6.6 Å

EMDB-21328:
Full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and 10E8v4-5R+100cF Fab
Method: EM (single particle) / Resolution: 7.8 Å

EMDB-21329:
Nanodisc of C-terminally truncated HIV-1 Envelope glycoprotein clone BG505 in complex with PGT151 Fab
Method: EM (single particle) / Resolution: 10.0 Å

EMDB-21330:
Ectodomain from nanodisc of C-terminally truncated HIV-1 Envelope glycoprotein clone BG505 in complex with PGT151 Fab
Method: EM (single particle) / Resolution: 4.6 Å

EMDB-21331:
Nanodisc of full-length HIV-1 Envelope glycoprotein clone PC64FL in complex with PGT151 Fab
Method: EM (single particle) / Resolution: 9.1 Å

EMDB-21332:
Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with two PGT151 Fabs and one 10E8 Fab
Method: EM (single particle) / Resolution: 6.5 Å

EMDB-21333:
Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with two PGT151 Fabs and three 10E8 Fabs
Method: EM (single particle) / Resolution: 9.4 Å

EMDB-21334:
Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and two 10E8 Fabs
Method: EM (single particle) / Resolution: 8.2 Å

21335

6vpx

EMDB-21335, PDB-6vpx:
Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 Fabs
Method: EM (single particle) / Resolution: 5.0 Å

EMDB-21336:
Full-length HIV-1 Envelope glycoprotein clone PC64 in DOPC-CHS bicelle
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-21337:
Complex of full-length HIV-1 Envelope glycoprotein clone PC64 and VRC42.01 Fab in DOPC-DOPS-CHS bicelle
Method: EM (single particle) / Resolution: 18.0 Å

EMDB-21338:
Complex of full-length HIV-1 Envelope glycoprotein clone PC64 and DH511.2 Fab in DOPC-DOPS-CHS bicelle
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-21339:
Complex of full-length HIV-1 Envelope glycoprotein clone PC64 and PGT151 Fab in DOPC-DOPS nanodisc
Method: EM (single particle) / Resolution: 18.0 Å

EMDB-21340:
Complex of full-length HIV-1 Envelope glycoprotein clone PC64 and VRC42.N1 Fab in DOPC-DOPS-CHS bicelle
Method: EM (single particle) / Resolution: 17.0 Å

EMDB-21341:
Complex of full-length HIV-1 Envelope glycoprotein clone AMC011 and VRC42.01 Fab in DOPC-DOPS-CHS nanodisc
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-21342:
Complex of full-length HIV-1 Envelope glycoprotein clone AMC011 and 10E8 Fab in nanodisc
Method: EM (single particle) / Resolution: 26.0 Å

EMDB-21343:
HIV-1 Envelope glycoprotein clone BG505-ST-710 in DOPC-DOPS-CHS peptidisc
Method: EM (single particle) / Resolution: 18.0 Å

EMDB-21344:
Complex of HIV-1 Envelope glycoprotein clone BG505-ST-710 and 10E8 Fab in DOPC-DOPS-CHS peptidisc
Method: EM (single particle) / Resolution: 20.0 Å

Chemicals

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

ChemComp-44E:
(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / phospholipid*YM

Source
  • homo sapiens (human)
  • human immunodeficiency virus 1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / Envelope glycoprotein / Env / neutralizing antibody / nanodisc / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex

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