[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

TitleStructural delineation of a quaternary, cleavage-dependent epitope at the gp41-gp120 interface on intact HIV-1 Env trimers.
Journal, issue, pagesImmunity, Vol. 40, Issue 5, Page 669-680, Year 2014
Publish dateMay 15, 2014
AuthorsClaudia Blattner / Jeong Hyun Lee / Kwinten Sliepen / Ronald Derking / Emilia Falkowska / Alba Torrents de la Peña / Albert Cupo / Jean-Philippe Julien / Marit van Gils / Peter S Lee / Wenjie Peng / James C Paulson / Pascal Poignard / Dennis R Burton / John P Moore / Rogier W Sanders / Ian A Wilson / Andrew B Ward /
PubMed AbstractAll previously characterized broadly neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) target one of four major sites of vulnerability. Here, we define and structurally characterize a ...All previously characterized broadly neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) target one of four major sites of vulnerability. Here, we define and structurally characterize a unique epitope on Env that is recognized by a recently discovered family of human monoclonal antibodies (PGT151-PGT158). The PGT151 epitope is comprised of residues and glycans at the interface of gp41 and gp120 within a single protomer and glycans from both subunits of a second protomer and represents a neutralizing epitope that is dependent on both gp120 and gp41. Because PGT151 binds only to properly formed, cleaved trimers, this distinctive property, and its ability to stabilize Env trimers, has enabled the successful purification of mature, cleaved Env trimers from the cell surface as a complex with PGT151. Here we compare the structural and functional properties of membrane-extracted Env trimers from several clades with those of the soluble, cleaved SOSIP gp140 trimer.
External linksImmunity / PubMed:24768348 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.827 - 25.0 Å
Structure data

EMDB-5918:
Negative stain reconstruction of PGT151 Fab in complex with BG505 Env with transmembrane region
Method: EM (single particle) / Resolution: 21.0 Å

EMDB-5919:
Negative stain reconstruction of PGT151 Fab in complex with JR-FL Env with transmembrane region
Method: EM (single particle) / Resolution: 19.0 Å

EMDB-5920:
Negative stain reconstruction of PGT151 Fab in complex with cleaved IAVI C22 Env trimer containing the transmembrane region
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-5921:
Negative stain reconstruction of PGT151 Fab in complex with the soluble Env trimer BG505 SOSIP
Method: EM (single particle) / Resolution: 22.0 Å

PDB-4nug:
Crystal structure of HIV-1 broadly neutralizing antibody PGT151
Method: X-RAY DIFFRACTION / Resolution: 1.8617 Å

PDB-4nuj:
Crystal structure of HIV-1 broadly neutralizing antibody PGT152
Method: X-RAY DIFFRACTION / Resolution: 1.827 Å

Chemicals

ChemComp-P6G:
HEXAETHYLENE GLYCOL / precipitant*YM

ChemComp-HOH:
WATER

Source
  • Human immunodeficiency virus 1
  • homo sapiens (human)
KeywordsIMMUNE SYSTEM / immunoglobulin / Fab fragment / HIV Envelope

+
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://pdbjlvh1.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