[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
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 / N-Acetylglucosamine

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

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more