[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

TitleLipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins.
Journal, issue, pagesJ Struct Biol, Vol. 215, Issue 3, Page 107989, Year 2023
Publish dateJun 24, 2023
AuthorsKevin S Cannon / Reta D Sarsam / Tanita Tedamrongwanish / Kevin Zhang / Richard W Baker /
PubMed AbstractPeripheral membrane proteins are ubiquitous throughout cell biology and are required for a variety of cellular processes such as signal transduction, membrane trafficking, and autophagy. Transient ...Peripheral membrane proteins are ubiquitous throughout cell biology and are required for a variety of cellular processes such as signal transduction, membrane trafficking, and autophagy. Transient binding to the membrane has a profound impact on protein function, serving to induce conformational changes and alter biochemical and biophysical parameters by increasing the local concentration of factors and restricting diffusion to two dimensions. Despite the centrality of the membrane in serving as a template for cell biology, there are few reported high-resolution structures of peripheral membrane proteins bound to the membrane. We analyzed the utility of lipid nanodiscs to serve as a template for cryo-EM analysis of peripheral membrane proteins. We tested a variety of nanodiscs and we report a 3.3 Å structure of the AP2 clathrin adaptor complex bound to a 17-nm nanodisc, with sufficient resolution to visualize a bound lipid head group. Our data demonstrate that lipid nanodiscs are amenable to high-resolution structure determination of peripheral membrane proteins and provide a framework for extending this analysis to other systems.
External linksJ Struct Biol / PubMed:37364761
MethodsEM (single particle)
Resolution3.3 - 6.8 Å
Structure data

EMDB-16803: AP2 bound to MSP1 nanodisc with Tgn38 cargo peptide
Method: EM (single particle) / Resolution: 4.9 Å

EMDB-16804: AP2 bound to MSP1E3D1 nanodisc with Tgn38 cargo peptide
Method: EM (single particle) / Resolution: 6.8 Å

EMDB-29977: AP2 bound to an MSP1 nanodisc
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-40034: Structure of AP2 bound to MSP1E3D1 nanodisc
Method: EM (single particle) / Resolution: 5.4 Å

EMDB-40035: Structure of AP2 bound to MSP2N2 nanodisc
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-40963: AP2 bound to MSP2N2 nanodisc with Tgn38 cargo peptide; focused refinement 1
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-40964: AP2 bound to MSP2N2 nanodisc with Tgn38 cargo peptide; focused refinement 2
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-40965: AP2 bound to MSP2N2 nanodisc with Tgn38 cargo peptide; focused refinement 3
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-40966: AP2 bound to MSP2N2 nanodisc with Tgn38 cargo peptide; consensus refinement
Method: EM (single particle) / Resolution: 3.4 Å

40973

8t1o

EMDB-40973, PDB-8t1o:
AP2 bound to MSP2N2 nanodisc with Tgn38 cargo peptide; composite map
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

Source
  • mus musculus (house mouse)
  • rattus norvegicus (Norway rat)
  • Homo sapiens (human)
KeywordsENDOCYTOSIS / Clathrin-mediated endocytosis; peripheral membrane protein

+
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