[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

TitleIntrinsically disordered CsoS2 acts as a general molecular thread for α-carboxysome shell assembly.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 5512, Year 2023
Publish dateSep 7, 2023
AuthorsTao Ni / Qiuyao Jiang / Pei Cing Ng / Juan Shen / Hao Dou / Yanan Zhu / Julika Radecke / Gregory F Dykes / Fang Huang / Lu-Ning Liu / Peijun Zhang /
PubMed AbstractCarboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the ...Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the disordered linker protein CsoS2 plays an essential role in carboxysome assembly and Rubisco encapsulation. Its mechanism of action, however, is not fully understood. Here we synthetically engineer α-carboxysome shells using minimal shell components and determine cryoEM structures of these to decipher the principle of shell assembly and encapsulation. The structures reveal that the intrinsically disordered CsoS2 C-terminus is well-structured and acts as a universal "molecular thread" stitching through multiple shell protein interfaces. We further uncover in CsoS2 a highly conserved repetitive key interaction motif, [IV]TG, which is critical to the shell assembly and architecture. Our study provides a general mechanism for the CsoS2-governed carboxysome shell assembly and cargo encapsulation and further advances synthetic engineering of carboxysomes for diverse biotechnological applications.
External linksNat Commun / PubMed:37679318 / PubMed Central
MethodsEM (single particle)
Resolution1.86 - 3.54 Å
Structure data

EMDB-15595: cryo-EM structure of carboxysomal mini-shell: oblate structure from C1 construct (T=7 Q=6)
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-15611: cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from C2 construct (T=4)
Method: EM (single particle) / Resolution: 2.26 Å

EMDB-15719: cryo-EM structure of carboxysome mini-shell: icosahedral structure from C1 construct (T=4)
Method: EM (single particle) / Resolution: 2.02 Å

EMDB-15720: cryo-EM structure of carboxysome mini-shell: icosahedral structure from C1 construct (T=7)
Method: EM (single particle) / Resolution: 3.29 Å

EMDB-15722: cryo-EM structure of carboxysome mini-shell: icosahedral structure from C1 construct (T=9)
Method: EM (single particle) / Resolution: 2.04 Å

EMDB-15723: cryo-EM structure of carboxysomal mini-shell: prolate structure from C1 construct (T=4 Q=6)
Method: EM (single particle) / Resolution: 2.65 Å

EMDB-15724: cryo-EM structure of carboxysomal mini-shell: prolate structure from C1 construct (T=4 Q=6) form 2
Method: EM (single particle) / Resolution: 2.69 Å

EMDB-15758: cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from C3 construct (T=4)
Method: EM (single particle) / Resolution: 2.39 Å

EMDB-15759: cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from C3 construct (T=4-P)
Method: EM (single particle) / Resolution: 3.28 Å

EMDB-15760: cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from C3 construct (T=3)
Method: EM (single particle) / Resolution: 2.31 Å

EMDB-15761: cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from C3 construct (T=3-P)
Method: EM (single particle) / Resolution: 2.68 Å

EMDB-15762: cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from C1 ITG mutant construct (T=4)
Method: EM (single particle) / Resolution: 2.65 Å

EMDB-15792: cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from CsoS4A-1A (T=4)
Method: EM (single particle) / Resolution: 3.54 Å

EMDB-15798, PDB-8b0y:
cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from CsoS4A/1A co-expression (T = 3)
Method: EM (single particle) / Resolution: 2.79 Å

EMDB-15799, PDB-8b11:
cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from CsoS4A/1A and CsoS2 co-expression (T = 4)
Method: EM (single particle) / Resolution: 2.52 Å

EMDB-15801, PDB-8b12:
cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from CsoS4A/1A and CsoS2 co-expression (T = 9)
Method: EM (single particle) / Resolution: 1.86 Å

EMDB-15834: cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from C1 ITG mutant construct (T=3)
Method: EM (single particle) / Resolution: 2.22 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • halothiobacillus neapolitanus (bacteria)
KeywordsSTRUCTURAL PROTEIN / carboxysome / shell / icosahedral symmetry

+
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