[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

TitleCryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains.
Journal, issue, pagesNat Commun, Vol. 8, Page 15092, Year 2017
Publish dateApr 10, 2017
AuthorsYuan Yuan / Duanfang Cao / Yanfang Zhang / Jun Ma / Jianxun Qi / Qihui Wang / Guangwen Lu / Ying Wu / Jinghua Yan / Yi Shi / Xinzheng Zhang / George F Gao /
PubMed AbstractThe envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and ...The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies.
External linksNat Commun / PubMed:28393837 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.5 - 4.2 Å
Structure data

EMDB-6703, PDB-5x58:
Prefusion structure of SARS-CoV spike glycoprotein, conformation 1
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-6704, PDB-5x59:
Prefusion structure of MERS-CoV spike glycoprotein, three-fold symmetry
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-6705, PDB-5x5b:
Prefusion structure of SARS-CoV spike glycoprotein, conformation 2
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-6706, PDB-5x5c:
Prefusion structure of MERS-CoV spike glycoprotein, conformation 1
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-6707, PDB-5x5f:
Prefusion structure of MERS-CoV spike glycoprotein, conformation 2
Method: EM (single particle) / Resolution: 4.2 Å

PDB-5x4r:
Structure of the N-terminal domain (NTD) of MERS-CoV spike protein
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-5x4s:
Structure of the N-terminal domain (NTD)of SARS-CoV spike protein
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

Chemicals

ChemComp-HOH:
WATER / Water

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • sars coronavirus bj01
  • middle east respiratory syndrome coronavirus
  • human sars coronavirus
KeywordsVIRAL PROTEIN / MERS-CoV / spike / N-terminal domain / SARS-CoV / spike glycoprotein / prefusion / single particle

+
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