[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 landscape of etioplast inner membranes in higher plants.
Journal, issue, pagesNat Plants, Vol. 7, Issue 4, Page 514-523, Year 2021
Publish dateApr 19, 2021
AuthorsDavide Floris / Werner Kühlbrandt /
PubMed AbstractEtioplasts are photosynthetically inactive plastids that accumulate when light levels are too low for chloroplast maturation. The etioplast inner membrane consists of a paracrystalline tubular ...Etioplasts are photosynthetically inactive plastids that accumulate when light levels are too low for chloroplast maturation. The etioplast inner membrane consists of a paracrystalline tubular lattice and peripheral, disk-shaped membranes, respectively known as the prolamellar body and prothylakoids. These distinct membrane regions are connected into one continuous compartment. To date, no structures of protein complexes in or at etioplast membranes have been reported. Here, we used electron cryo-tomography to explore the molecular membrane landscape of pea and maize etioplasts. Our tomographic reconstructions show that ATP synthase monomers are enriched in the prothylakoids, and plastid ribosomes in the tubular lattice. The entire tubular lattice is covered by regular helical arrays of a membrane-associated protein, which we identified as the 37-kDa enzyme, light-dependent protochlorophyllide oxidoreductase (LPOR). LPOR is the most abundant protein in the etioplast, where it is responsible for chlorophyll biosynthesis, photoprotection and defining the membrane geometry of the prolamellar body. Based on the 9-Å-resolution volume of the subtomogram average, we propose a structural model of membrane-associated LPOR.
External linksNat Plants / PubMed:33875833 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution9.0 - 29.9 Å
Structure data

EMDB-11958:
Cryo-EM map of the ATP synthase complex from P. sativum
Method: EM (subtomogram averaging) / Resolution: 29.9 Å

EMDB-11959:
Cryo-EM map of the chloroplast ribosome from P. sativum
Method: EM (subtomogram averaging) / Resolution: 26.0 Å

EMDB-11960:
Cryo-EM map of the membrane-associated light-dependent protochlorophyllide oxidoreductase (LPOR) from Z. mays (helical arrays, 15 units per turn)
Method: EM (subtomogram averaging) / Resolution: 18.1 Å

EMDB-11961:
Cryo-EM map of the membrane-associated light-dependent protochlorophyllide oxidoreductase (LPOR) from Z. mays (helical arrays, 16 units per turn)
Method: EM (subtomogram averaging) / Resolution: 18.2 Å

EMDB-11962:
Cryo-EM map of the membrane-associated light-dependent protochlorophyllide oxidoreductase (LPOR) from Z. mays (subboxed helical arrays, 15 units per turn)
Method: EM (subtomogram averaging) / Resolution: 9.0 Å

EMDB-11963:
Cryo-EM map of the membrane-associated light-dependent protochlorophyllide oxidoreductase (LPOR) from Z. mays (subboxed helical arrays, 16 units per turn)
Method: EM (subtomogram averaging) / Resolution: 9.1 Å

Source
  • Pisum sativum (garden pea)
  • Zea mays (maize)

+
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