[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

TitleRapid and High-Throughput Imaging of Immune Complexes Using Microfluidics and Single Particle Electron Microscopy
Journal, issue, pagesNat Biomed Eng, Year 2025
Publish dateApr 30, 2024 (structure data deposition date)
AuthorsSewall LM / de Paiva Froes Rocha R / Gibson G / Louie M / Xie Z / Bangaru S / Tran AS / Ozorowski G / Mohanty S / Beutler N ...Sewall LM / de Paiva Froes Rocha R / Gibson G / Louie M / Xie Z / Bangaru S / Tran AS / Ozorowski G / Mohanty S / Beutler N / Burton DR / Shaw AC / Batista FD / Chocarro Ruiz B / Torrents de la Pena A / Ward AB
External linksSearch PubMed
MethodsEM (single particle)
Resolution3.1 - 26.0 Å
Structure data

EMDB-44655: Representative polyclonal epitopes targeted on HA H1 protein with complexing by conventional EMPEM
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44656: Representative polyclonal epitopes targeted on HA Influenza B protein with complexing by conventional EMPEM
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44657: Representative polyclonal epitopes targeted on CoV OC43 spike protein with conventional EMPEM complexing
Method: EM (single particle) / Resolution: 20.0 Å

44658

9blk

EMDB-44658, PDB-9blk:
HCoV-OC43 Spike glycoprotein
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-44659: Representative polyclonal epitopes targeted on CoV HKU1 spike protein with conventional EMPEM complexing
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44660: Representative polyclonal epitopes targeted on SARS-CoV-2 spike protein with conventional EMPEM complexing
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44661: Representative polyclonal epitopes targeted on HA H1 protein with complexing by mEM
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44662: Representative polyclonal epitopes targeted on HA Influenza B protein with complexing by mEM
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44663: Representative polyclonal epitopes targeted on CoV OC43 spike protein with complexing by mEM
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44664: Representative polyclonal epitopes targeted on CoV HKU1 spike protein with complexing by mEM
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44665: Representative polyclonal epitopes targeted on SARS-CoV-2 spike protein with complexing by mEM
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44667: CoV SARS-2 spike protein complexed by mEM with monoclonal antibody TXG-0078 Fab
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44669: HIV Env BG505.SOSIP N332-GT5 protein complexed by mEM with polyclonal Fab representative of Group 1
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44670: HIV Env BG505.SOSIP N332-GT5 protein complexed by mEM with polyclonal Fab representative of Group 2
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-44679: SARS-CoV-2 S glycoprotein in closed state
Method: EM (single particle) / Resolution: 4.6 Å

EMDB-44680: SARS-Cov-2 spike glycoprotein with 1 RBD up
Method: EM (single particle) / Resolution: 6.9 Å

EMDB-44882: CoV OC43 S glycoprotein in complex with polyclonal antibodies from donor 2327 at day 7
Method: EM (single particle) / Resolution: 24.9 Å

EMDB-44883: Influenza hemagglutinin B/Maryland/2016 in complex with polyclonal antibodies from donor 2323 at day 7
Method: EM (single particle) / Resolution: 26.0 Å

44894

9bto

EMDB-44894, PDB-9bto:
Influenza hemagglutinin B/Maryland/2016 glycoprotein
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

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

Source
  • Influenza A virus
  • human coronavirus oc43
  • Human coronavirus HKU1
  • Severe acute respiratory syndrome coronavirus 2
  • Human immunodeficiency virus 1
  • influenza b virus
KeywordsVIRAL PROTEIN / HCoV / cryoEM / microfluidics / hemagglutinin / influenza / 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