[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 SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Journal, issue, pagesCell Host Microbe, Vol. 28, Issue 6, Page 867-879.e5, Year 2020
Publish dateDec 9, 2020
AuthorsTongqing Zhou / Yaroslav Tsybovsky / Jason Gorman / Micah Rapp / Gabriele Cerutti / Gwo-Yu Chuang / Phinikoula S Katsamba / Jared M Sampson / Arne Schön / Jude Bimela / Jeffrey C Boyington / Alexandra Nazzari / Adam S Olia / Wei Shi / Mallika Sastry / Tyler Stephens / Jonathan Stuckey / I-Ting Teng / Pengfei Wang / Shuishu Wang / Baoshan Zhang / Richard A Friesner / David D Ho / John R Mascola / Lawrence Shapiro / Peter D Kwong /
PubMed AbstractThe SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand ...The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand how ACE2 binding and low pH affect spike conformation, we determined cryo-electron microscopy structures-at serological and endosomal pH-delineating spike recognition of up to three ACE2 molecules. RBDs freely adopted "up" conformations required for ACE2 interaction, primarily through RBD movement combined with smaller alterations in neighboring domains. In the absence of ACE2, single-RBD-up conformations dominated at pH 5.5, resolving into a solitary all-down conformation at lower pH. Notably, a pH-dependent refolding region (residues 824-858) at the spike-interdomain interface displayed dramatic structural rearrangements and mediated RBD positioning through coordinated movements of the entire trimer apex. These structures provide a foundation for understanding prefusion-spike mechanics governing endosomal entry; we suggest that the low pH all-down conformation potentially facilitates immune evasion from RBD-up binding antibody.
External linksCell Host Microbe / PubMed:33271067 / PubMed Central
MethodsEM (single particle)
Resolution2.4 - 3.93 Å
Structure data

EMDB-22251, PDB-6xlu:
Structure of SARS-CoV-2 spike at pH 4.0
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-22253, PDB-6xm0:
Consensus structure of SARS-CoV-2 spike at pH 5.5
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-22254, PDB-6xm3:
Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 1
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-22255, PDB-6xm4:
Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 2
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-22256, PDB-6xm5:
Structure of SARS-CoV-2 spike at pH 5.5, all RBDs down
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-22515, PDB-7jwy:
Structure of SARS-CoV-2 spike at pH 4.5
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-22922, PDB-7kmb:
ACE2-RBD Focused Refinement Using Symmetry Expansion of Applied C3 for Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 7.4
Method: EM (single particle) / Resolution: 3.39 Å

EMDB-22927, PDB-7kms:
Cryo-EM structure of triple ACE2-bound SARS-CoV-2 trimer spike at pH 7.4
Method: EM (single particle) / Resolution: 3.64 Å

EMDB-22932, PDB-7kmz:
Cryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at pH 7.4
Method: EM (single particle) / Resolution: 3.62 Å

EMDB-22941, PDB-7knb:
Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 7.4
Method: EM (single particle) / Resolution: 3.93 Å

EMDB-22943, PDB-7kne:
Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 5.5
Method: EM (single particle) / Resolution: 3.85 Å

EMDB-22949, PDB-7knh:
Cryo-EM Structure of Double ACE2-Bound SARS-CoV-2 Trimer Spike at pH 5.5
Method: EM (single particle) / Resolution: 3.74 Å

EMDB-22950, PDB-7kni:
Cryo-EM structure of Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 5.5
Method: EM (single particle) / Resolution: 3.91 Å

Chemicals

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

ChemComp-HOH:
WATER

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / SARS-CoV-2 spike COVID19 / SARS-CoV-2 spike / COVID19 / SARS-CoV-2 COVID19 / Hydrolase/Viral Protein / COVID / SARS-CoV2 / ACE2 / prefusion / Hydrolase-Viral Protein complex / VIRAL PROTEIN/Hydrolase / VIRAL PROTEIN-Hydrolase 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