[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

TitleStaged induction of HIV-1 glycan-dependent broadly neutralizing antibodies.
Journal, issue, pagesSci Transl Med, Vol. 9, Issue 381, Year 2017
Publish dateMar 15, 2017
AuthorsMattia Bonsignori / Edward F Kreider / Daniela Fera / R Ryan Meyerhoff / Todd Bradley / Kevin Wiehe / S Munir Alam / Baptiste Aussedat / William E Walkowicz / Kwan-Ki Hwang / Kevin O Saunders / Ruijun Zhang / Morgan A Gladden / Anthony Monroe / Amit Kumar / Shi-Mao Xia / Melissa Cooper / Mark K Louder / Krisha McKee / Robert T Bailer / Brendan W Pier / Claudia A Jette / Garnett Kelsoe / Wilton B Williams / Lynn Morris / John Kappes / Kshitij Wagh / Gift Kamanga / Myron S Cohen / Peter T Hraber / David C Montefiori / Ashley Trama / Hua-Xin Liao / Thomas B Kepler / M Anthony Moody / Feng Gao / Samuel J Danishefsky / John R Mascola / George M Shaw / Beatrice H Hahn / Stephen C Harrison / Bette T Korber / Barton F Haynes /
PubMed AbstractA preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and ...A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and current vaccine strategies have not been successful in inducing bnAbs. Because bnAbs directed against a glycosylated site adjacent to the third variable loop (V3) of the HIV-1 envelope protein require limited SHM, the V3-glycan epitope is an attractive vaccine target. By studying the cooperation among multiple V3-glycan B cell lineages and their coevolution with autologous virus throughout 5 years of infection, we identify key events in the ontogeny of a V3-glycan bnAb. Two autologous neutralizing antibody lineages selected for virus escape mutations and consequently allowed initiation and affinity maturation of a V3-glycan bnAb lineage. The nucleotide substitution required to initiate the bnAb lineage occurred at a low-probability site for activation-induced cytidine deaminase activity. Cooperation of B cell lineages and an improbable mutation critical for bnAb activity defined the necessary events leading to breadth in this V3-glycan bnAb lineage. These findings may, in part, explain why initiation of V3-glycan bnAbs is rare, and suggest an immunization strategy for inducing similar V3-glycan bnAbs.
External linksSci Transl Med / PubMed:28298420 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.85 - 29.4 Å
Structure data

EMDB-8507:
92BR SOSIP.664 trimer in complex with DH270.1 Fab
Method: EM (single particle) / Resolution: 29.4 Å

PDB-5tpl:
Crystal Structure of DH270.3 (unliganded) from the DH270 Broadly Neutralizing N332-glycan Dependent Lineage
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-5tpp:
Crystal Structure of DH270.5 (unliganded) from the DH270 Broadly Neutralizing N332-glycan Dependent Lineage
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-5tqa:
Crystal Structure of DH270.6 (unliganded) from the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage
Method: X-RAY DIFFRACTION / Resolution: 2.723 Å

PDB-5trp:
Crystal Structure of the Unliganded DH270 Cooperating Lineage Member DH272
Method: X-RAY DIFFRACTION / Resolution: 2.692 Å

PDB-5u0r:
Crystal Structure of DH270.UCA1 (unliganded) from the DH270 Broadly Neutralizing N332-glycan Dependent Lineage
Method: X-RAY DIFFRACTION / Resolution: 3.295 Å

PDB-5u0u:
Crystal Structure of DH270.1 (unliganded, single-chain Fv) from the DH270 Broadly Neutralizing N332-glycan Dependent Lineage
Method: X-RAY DIFFRACTION / Resolution: 3.428 Å

PDB-5u15:
Crystal Structure of DH270.UCA3 (unliganded) from the DH270 Broadly Neutralizing N332-glycan Dependent Lineage
Method: X-RAY DIFFRACTION / Resolution: 2.26 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-NA:
Unknown entry

ChemComp-CIT:
CITRIC ACID

ChemComp-SO4:
SULFATE ION

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

Source
  • Human immunodeficiency virus 1
  • homo sapiens (human)
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / HIV-1 / ANTIBODY / single-chain variable fragment

+
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