[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

TitleStructural snapshots uncover a key phosphorylation motif in GPCRs driving β-arrestin activation.
Journal, issue, pagesMol Cell, Vol. 83, Issue 12, Page 2091-22107.e7, Year 2023
Publish dateJun 15, 2023
AuthorsJagannath Maharana / Parishmita Sarma / Manish K Yadav / Sayantan Saha / Vinay Singh / Shirsha Saha / Mohamed Chami / Ramanuj Banerjee / Arun K Shukla /
PubMed AbstractAgonist-induced GPCR phosphorylation is a key determinant for the binding and activation of β-arrestins (βarrs). However, it is not entirely clear how different GPCRs harboring divergent ...Agonist-induced GPCR phosphorylation is a key determinant for the binding and activation of β-arrestins (βarrs). However, it is not entirely clear how different GPCRs harboring divergent phosphorylation patterns impart converging active conformation on βarrs leading to broadly conserved functional responses such as desensitization, endocytosis, and signaling. Here, we present multiple cryo-EM structures of activated βarrs in complex with distinct phosphorylation patterns derived from the carboxyl terminus of different GPCRs. These structures help identify a P-X-P-P type phosphorylation motif in GPCRs that interacts with a spatially organized K-K-R-R-K-K sequence in the N-domain of βarrs. Sequence analysis of the human GPCRome reveals the presence of this phosphorylation pattern in a large number of receptors, and its contribution in βarr activation is demonstrated by targeted mutagenesis experiments combined with an intrabody-based conformational sensor. Taken together, our findings provide important structural insights into the ability of distinct GPCRs to activate βarrs through a significantly conserved mechanism.
External linksMol Cell / PubMed:37209686 / PubMed Central
MethodsEM (single particle)
Resolution3.26 - 4.8 Å
Structure data

34173

8go8

EMDB-34173, PDB-8go8:
Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1
Method: EM (single particle) / Resolution: 3.41 Å

34175

8goc

EMDB-34175, PDB-8goc:
Structure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human Vasopressin V2 receptor, V2R
Method: EM (single particle) / Resolution: 4.18 Å

34178

8goo

EMDB-34178, PDB-8goo:
Structure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1
Method: EM (single particle) / Resolution: 4.4 Å

34188

8gp3

EMDB-34188, PDB-8gp3:
Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4
Method: EM (single particle) / Resolution: 4.8 Å

35104

8i0n

EMDB-35104, PDB-8i0n:
Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 (Local refine)
Method: EM (single particle) / Resolution: 3.26 Å

35106

8i0q

EMDB-35106, PDB-8i0q:
Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4 (Local refine)
Method: EM (single particle) / Resolution: 4.45 Å

35114

8i0z

EMDB-35114, PDB-8i0z:
Structure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 (Local refine)
Method: EM (single particle) / Resolution: 4.33 Å

35115

8i10

EMDB-35115, PDB-8i10:
Structure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human Vasopressin V2 receptor, V2R (Local refine)
Method: EM (single particle) / Resolution: 3.96 Å

Source
  • rattus norvegicus (Norway rat)
  • homo sapiens (human)
  • mus musculus (house mouse)
  • bos taurus (cattle)
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / Arrestin / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM 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://pdbjlvh1.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