[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

TitleDual Functions of a Rubisco Activase in Metabolic Repair and Recruitment to Carboxysomes.
Journal, issue, pagesCell, Vol. 183, Issue 2, Page 457-473.e20, Year 2020
Publish dateOct 15, 2020
AuthorsMirkko Flecken / Huping Wang / Leonhard Popilka / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl /
PubMed AbstractRubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone ...Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone Rubisco activase (Rca) in a process that is not well understood. Here, we performed a structural and mechanistic analysis of cyanobacterial Rca, a close homolog of plant Rca. In the Rca:Rubisco complex, Rca is positioned over the Rubisco catalytic site under repair and pulls the N-terminal tail of the large Rubisco subunit (RbcL) into the hexamer pore. Simultaneous displacement of the C terminus of the adjacent RbcL opens the catalytic site for inhibitor release. An alternative interaction of Rca with Rubisco is mediated by C-terminal domains that resemble the small Rubisco subunit. These domains, together with the N-terminal AAA+ hexamer, ensure that Rca is packaged with Rubisco into carboxysomes. The cyanobacterial Rca is a dual-purpose protein with functions in Rubisco repair and carboxysome organization.
External linksCell / PubMed:32979320
MethodsEM (single particle) / X-ray diffraction
Resolution1.38 - 8.2 Å
Structure data

11028

6z1f

EMDB-11028, PDB-6z1f:
CryoEM structure of Rubisco Activase with its substrate Rubisco from Nostoc sp. (strain PCC7120)
Method: EM (single particle) / Resolution: 2.86 Å

11029

6z1g

EMDB-11029, PDB-6z1g:
CryoEM structure of the interaction between Rubisco Activase small-subunit-like (SSUL) domain with Rubisco from Nostoc sp. (strain PCC7120)
Method: EM (single particle) / Resolution: 8.2 Å

EMDB-11575:
CryoEM Local map of Rubisco Activase from the complex with its substrate Rubisco from Nostoc sp. (strain PCC7120)
Method: EM (single particle) / Resolution: 3.29 Å

PDB-6has:
Crystal Structure of the small subunit-like domain of Rubisco activase from Nostoc sp. (strain PCC 7120)
Method: X-RAY DIFFRACTION / Resolution: 1.38 Å

PDB-6z1d:
Crystal structure of the AAA domain of Rubisco Activase from Nostoc sp. (strain PCC 7120), Gadolinium complex
Method: X-RAY DIFFRACTION / Resolution: 2.705 Å

PDB-6z1e:
Crystal structure of the AAA domain of Rubisco Activase from Nostoc sp. (strain PCC 7120)
Method: X-RAY DIFFRACTION / Resolution: 2.454 Å

Chemicals

ChemComp-NI:
NICKEL (II) ION / Nickel

ChemComp-HOH:
WATER / Water

ChemComp-GD:
GADOLINIUM ATOM

ChemComp-CL:
Unknown entry / Chloride

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-CAP:
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

Source
  • nostoc sp. pcc 7120 = fachb-418 (bacteria)
  • nostoc sp. (strain pcc 7120 / sag 25.82 / utex 2576) (bacteria)
KeywordsCHAPERONE / alpha-beta structure / Rubisco / AAA+ domain / AAA+ / beta barrel / PHOTOSYNTHESIS

+
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