[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

TitleStructure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.
Journal, issue, pagesScience, Vol. 371, Issue 6530, Year 2021
Publish dateFeb 12, 2021
AuthorsPaul-Albert Koenig / Hrishikesh Das / Hejun Liu / Beate M Kümmerer / Florian N Gohr / Lea-Marie Jenster / Lisa D J Schiffelers / Yonas M Tesfamariam / Miki Uchima / Jennifer D Wuerth / Karl Gatterdam / Natalia Ruetalo / Maria H Christensen / Caroline I Fandrey / Sabine Normann / Jan M P Tödtmann / Steffen Pritzl / Leo Hanke / Jannik Boos / Meng Yuan / Xueyong Zhu / Jonathan L Schmid-Burgk / Hiroki Kato / Michael Schindler / Ian A Wilson / Matthias Geyer / Kerstin U Ludwig / B Martin Hällberg / Nicholas C Wu / Florian I Schmidt /
PubMed AbstractThe pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread, with devastating consequences. For passive immunization efforts, nanobodies have size and cost ...The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread, with devastating consequences. For passive immunization efforts, nanobodies have size and cost advantages over conventional antibodies. In this study, we generated four neutralizing nanobodies that target the receptor binding domain of the SARS-CoV-2 spike protein. We used x-ray crystallography and cryo-electron microscopy to define two distinct binding epitopes. On the basis of these structures, we engineered multivalent nanobodies with more than 100 times the neutralizing activity of monovalent nanobodies. Biparatopic nanobody fusions suppressed the emergence of escape mutants. Several nanobody constructs neutralized through receptor binding competition, whereas other monovalent and biparatopic nanobodies triggered aberrant activation of the spike fusion machinery. These premature conformational changes in the spike protein forestalled productive fusion and rendered the virions noninfectious.
External linksScience / PubMed:33436526 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.87 - 4.01 Å
Structure data

11978

7b14

EMDB-11978: Nanobody E bound to Spike-RBD in a localized reconstruction.
PDB-7b14: Nanobody E bound to Spike-RBD in a localized reconstruction
Method: EM (single particle) / Resolution: 3.79 Å

11980

7b17

EMDB-11980: SARS-CoV-spike RBD bound to two neutralising nanobodies
PDB-7b17: SARS-CoV-spike RBD bound to two neutralising nanobodies.
Method: EM (single particle) / Resolution: 4.01 Å

11981

7b18

EMDB-11981, PDB-7b18:
SARS-CoV-spike bound to two neutralising nanobodies
Method: EM (single particle) / Resolution: 2.62 Å

23018

7ksg

EMDB-23018, PDB-7ksg:
SARS-CoV-2 spike in complex with nanobodies E
Method: EM (single particle) / Resolution: 3.33 Å

PDB-7kn5:
Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

PDB-7kn6:
Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-7kn7:
Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and antibody Fab CC12.3
Method: X-RAY DIFFRACTION / Resolution: 2.73 Å

Chemicals

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

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-HOH:
WATER

Source
  • severe acute respiratory syndrome coronavirus 2
  • camelus bactrianus (Bactrian camel)
  • vicugna pacos (alpaca)
  • lama glama (llama)
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / spike glycoprotein / SARS-CoV-2 / nanobody / VIRAL PROTEIN/IMMUNE SYSTEM / Spike / Coronavirus / COVID-19 / IMMUNE SYSTEM / Nanobody-antigen complex / single-domain antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex / Antibody / spike protein / VIRUS

+
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