[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

TitleDiverse Antibody Responses to Conserved Structural Motifs in Plasmodium falciparum Circumsporozoite Protein.
Journal, issue, pagesJ Mol Biol, Vol. 432, Issue 4, Page 1048-1063, Year 2020
Publish dateFeb 14, 2020
AuthorsTossapol Pholcharee / David Oyen / Jonathan L Torres / Yevel Flores-Garcia / Gregory M Martin / Gonzalo E González-Páez / Daniel Emerling / Wayne Volkmuth / Emily Locke / C Richter King / Fidel Zavala / Andrew B Ward / Ian A Wilson /
PubMed AbstractMalaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 ...Malaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 clinical trial, and it protects mice from infection by malaria sporozoites. However, mAb397 originates from the less commonly used VH3-15 germline gene compared to the VH3-30/33 antibodies generally elicited by RTS,S to the central NANP repeat region of CSP. The crystal structure of mAb397 with an NPNA peptide shows that the central NPNA forms a type I β-turn and is the main recognition motif. In most anti-NANP antibodies studied to date, a germline-encoded Trp is used to engage the Pro in NPNA β-turns, but here the Trp interacts with the first Asn. This "conserved" Trp, however, can arise from different germline genes and be located in the heavy or the light chain. Variation in the terminal ψ angles of the NPNA β-turns results in different dispositions of the subsequent NPNA and, hence, different stoichiometries and modes of antibody binding to rsCSP. Diverse protective antibodies against NANP repeats are therefore not limited to a single germline gene response or mode of binding.
External linksJ Mol Biol / PubMed:31883801 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.75 - 31.0 Å
Structure data

EMDB-20772:
Fab397 in complex with NPNA8 peptide (Class 1)
Method: EM (single particle) / Resolution: 24.0 Å

EMDB-20773:
Fab397 in complex with NPNA8 peptide (Class 2)
Method: EM (single particle) / Resolution: 21.0 Å

EMDB-20774:
Fab397 in complex with NPNA8 peptide (Class 3)
Method: EM (single particle) / Resolution: 27.0 Å

EMDB-20775:
Fab397 in complex with rsCSP (Class 1)
Method: EM (single particle) / Resolution: 28.0 Å

EMDB-20776:
Fab397 in complex with rsCSP (Class 2)
Method: EM (single particle) / Resolution: 27.0 Å

EMDB-20777:
Fab397 in complex with rsCSP (Class 3)
Method: EM (single particle) / Resolution: 28.0 Å

EMDB-20778:
Fab397 in complex with rsCSP (Class 4)
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-20779:
Fab397 in complex with rsCSP (Class 5)
Method: EM (single particle) / Resolution: 31.0 Å

EMDB-20780:
Fab397 in complex with rsCSP (Class 6)
Method: EM (single particle) / Resolution: 31.0 Å

PDB-6uc5:
Fab397 in complex with NPNA peptide
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
  • Plasmodium falciparum (malaria parasite P. falciparum)
  • plasmodium falciparum 3d7 (eukaryote)
KeywordsIMMUNE SYSTEM / Antibody / Malaria / Circumsporozoite protein / CSP / NANP / NANP repeats / Plasmodium / Plasmodium falciparum

+
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