[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

TitleCryomicroscopy reveals the structural basis for a flexible hinge motion in the immunoglobulin M pentamer.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 6314, Year 2022
Publish dateOct 23, 2022
AuthorsQu Chen / Rajesh Menon / Lesley J Calder / Pavel Tolar / Peter B Rosenthal /
PubMed AbstractImmunoglobulin M (IgM) is the most ancient of the five isotypes of immunoglobulin (Ig) molecules and serves as the first line of defence against pathogens. Here, we use cryo-EM to image the structure ...Immunoglobulin M (IgM) is the most ancient of the five isotypes of immunoglobulin (Ig) molecules and serves as the first line of defence against pathogens. Here, we use cryo-EM to image the structure of the human full-length IgM pentamer, revealing antigen binding domains flexibly attached to the asymmetric and rigid core formed by the Cμ4 and Cμ3 constant regions and the J-chain. A hinge is located at the Cμ3/Cμ2 domain interface, allowing Fabs and Cμ2 to pivot as a unit both in-plane and out-of-plane. This motion is different from that observed in IgG and IgA, where the two Fab arms are able to swing independently. A biased orientation of one pair of Fab arms results from asymmetry in the constant domain (Cμ3) at the IgM subunit interacting most extensively with the J-chain. This may influence the multi-valent binding to surface-associated antigens and complement pathway activation. By comparison, the structure of the Fc fragment in the IgM monomer is similar to that of the pentamer, but is more dynamic in the Cμ4 domain.
External linksNat Commun / PubMed:36274064 / PubMed Central
MethodsEM (single particle)
Resolution3.6 - 8.5 Å
Structure data

EMDB-13921: Cryo-EM structure of full-length human immunoglobulin M
Method: EM (single particle) / Resolution: 4.4 Å

13922

7qdo

EMDB-13922, PDB-7qdo:
Cryo-EM structure of human monomeric IgM-Fc
Method: EM (single particle) / Resolution: 3.6 Å

15375

8ady

EMDB-15375, PDB-8ady:
Cryo-EM structure of full-length human immunoglobulin M - F(ab')2 conformation 1
Method: EM (single particle) / Resolution: 5.2 Å

15376

8adz

EMDB-15376, PDB-8adz:
Cryo-EM structure of full-length human immunoglobulin M - F(ab')2 conformation 2
Method: EM (single particle) / Resolution: 6.7 Å

15377

8ae0

EMDB-15377, PDB-8ae0:
Cryo-EM structure of full-length human immunoglobulin M - F(ab')2 conformation 3
Method: EM (single particle) / Resolution: 7.1 Å

15379

8ae2

EMDB-15379, PDB-8ae2:
Cryo-EM structure of full-length human immunoglobulin M - F(ab')2 conformation 5
Method: EM (single particle) / Resolution: 8.5 Å

15380

8ae3

EMDB-15380, PDB-8ae3:
Cryo-EM structure of full-length human immunoglobulin M - F(ab')2 conformation 4
Method: EM (single particle) / Resolution: 6.8 Å

Chemicals

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

Source
  • homo sapiens (human)
  • human (human)
KeywordsIMMUNE SYSTEM / human monomeric IgM-Fc / full-length human immunoglobulin M

+
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