[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

TitleMolecular basis of anaphylatoxin binding, activation, and signaling bias at complement receptors.
Journal, issue, pagesCell, Vol. 186, Issue 22, Page 4956-4973.e21, Year 2023
Publish dateOct 26, 2023
AuthorsManish K Yadav / Jagannath Maharana / Ravi Yadav / Shirsha Saha / Parishmita Sarma / Chahat Soni / Vinay Singh / Sayantan Saha / Manisankar Ganguly / Xaria X Li / Samanwita Mohapatra / Sudha Mishra / Htet A Khant / Mohamed Chami / Trent M Woodruff / Ramanuj Banerjee / Arun K Shukla / Cornelius Gati /
PubMed AbstractThe complement system is a critical part of our innate immune response, and the terminal products of this cascade, anaphylatoxins C3a and C5a, exert their physiological and pathophysiological ...The complement system is a critical part of our innate immune response, and the terminal products of this cascade, anaphylatoxins C3a and C5a, exert their physiological and pathophysiological responses primarily via two GPCRs, C3aR and C5aR1. However, the molecular mechanism of ligand recognition, activation, and signaling bias of these receptors remains mostly elusive. Here, we present nine cryo-EM structures of C3aR and C5aR1 activated by their natural and synthetic agonists, which reveal distinct binding pocket topologies of complement anaphylatoxins and provide key insights into receptor activation and transducer coupling. We also uncover the structural basis of a naturally occurring mechanism to dampen the inflammatory response of C5a via proteolytic cleavage of the terminal arginine and the G-protein signaling bias elicited by a peptide agonist of C3aR identified here. In summary, our study elucidates the innerworkings of the complement anaphylatoxin receptors and should facilitate structure-guided drug discovery to target these receptors in a spectrum of disorders.
External linksCell / PubMed:37852260 / PubMed Central
MethodsEM (single particle)
Resolution2.88 - 4.55 Å
Structure data

34943

8hpt

EMDB-34943, PDB-8hpt:
Structure of C5a-pep bound mouse C5aR1 in complex with Go
Method: EM (single particle) / Resolution: 3.39 Å

34947

8hqc

EMDB-34947, PDB-8hqc:
Structure of a GPCR-G protein in complex with a natural peptide agonist
Method: EM (single particle) / Resolution: 3.89 Å

35257

8i95

EMDB-35257, PDB-8i95:
Structure of EP54-C3aR-Go complex
Method: EM (single particle) / Resolution: 2.88 Å

35259

8i97

EMDB-35259, PDB-8i97:
Structure of Apo-C3aR-Go complex (Glacios)
Method: EM (single particle) / Resolution: 3.19 Å

35263

8i9a

EMDB-35263, PDB-8i9a:
Structure of EP54-C3aR-Gq complex
Method: EM (single particle) / Resolution: 3.57 Å

35275

8i9l

EMDB-35275, PDB-8i9l:
Structure of C3a-C3aR-Go complex (Composite map)
Method: EM (single particle) / Resolution: 3.18 Å

35282

8i9s

EMDB-35282, PDB-8i9s:
Structure of Apo-C3aR-Go complex (Titan)
Method: EM (single particle) / Resolution: 3.26 Å

35292

8ia2

EMDB-35292, PDB-8ia2:
Structure of C5a bound human C5aR1 in complex with Go (Composite map)
Method: EM (single particle) / Resolution: 3.21 Å

EMDB-35293: C3a-C3aR-Go (C3aR-Go complex only, Original Map)
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-35294: C3a-C3aR-Go (C3a only, Original Map)
Method: EM (single particle) / Resolution: 4.55 Å

EMDB-35295: C5a-hC5aR1-Go (hC5aR1-Go complex only, Original map)
Method: EM (single particle) / Resolution: 3.21 Å

EMDB-35296: C5a-hC5aR1-Go complex (C5a only, Original map)
Method: EM (single particle) / Resolution: 3.88 Å

36001

8j6d

EMDB-36001, PDB-8j6d:
Structure of EP141-C3aR-Go complex
Method: EM (single particle) / Resolution: 3.1 Å

36755

8jzz

EMDB-36755, PDB-8jzz:
Structure of human C5a-desArg bound human C5aR1 in complex with Go
Method: EM (single particle) / Resolution: 3.31 Å

Source
  • mus musculus (house mouse)
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsSIGNATLING PROTEIN/IMMUNE SYSTEM / GPCR / G protein / SIGNALING PROTEIN / SIGNATLING PROTEIN-IMMUNE SYSTEM complex / SIGNALING PROTEIN/IMMUNE SYSTEM / SIGNALING PROTEIN-IMMUNE SYSTEM complex / Cell Signaling / Immune system

+
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