[English] 日本語
Yorodumi
- EMDB-64946: Map including micelle density from the photosynthetic LH1-RC comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64946
TitleMap including micelle density from the photosynthetic LH1-RC complex of the halophilic nonsulfur purple bacterium Rhodothalassium salexigens
Map dataMap including micelle density from the photosynthetic LH1-RC complex of the halophilic nonsulfur purple bacterium Rhodothalassium salexigens
Sample
  • Complex: LH1-RC complex of Rhodothalassium salexigens
KeywordsLH1-RC / Photocomplex / Halophilic Nonsulfur Purple Bacterium / PHOTOSYNTHESIS
Biological speciesRhodothalassium salexigens DSM 2132 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsTani K / Kanno R / Inami M / Ooya T / Matsushita R / Inada K / Takenaka S / Takaichi S / Purba ER / Hall M ...Tani K / Kanno R / Inami M / Ooya T / Matsushita R / Inada K / Takenaka S / Takaichi S / Purba ER / Hall M / Mochizuki T / Yu L-J / Mizoguchi A / Humbel BM / Madigan MT / Kimura Y / Wang-Otomo Z-Y
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121004 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101116 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Society for the Promotion of Science (JSPS)20H05086 Japan
Japan Society for the Promotion of Science (JSPS)20H02856 Japan
Japan Society for the Promotion of Science (JSPS)22K06111 Japan
CitationJournal: Biochemistry / Year: 2025
Title: Structure and Biochemistry of the LH1-RC Photocomplex from the Halophilic Purple Bacterium, .
Authors: Kazutoshi Tani / Ryo Kanno / Miyu Inami / Takumi Ooya / Ryo Matsushita / Kazuki Inada / Shinji Takenaka / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / Toshiaki Mochizuki / Long- ...Authors: Kazutoshi Tani / Ryo Kanno / Miyu Inami / Takumi Ooya / Ryo Matsushita / Kazuki Inada / Shinji Takenaka / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / Toshiaki Mochizuki / Long-Jiang Yu / Akira Mizoguchi / Bruno M Humbel / Michael T Madigan / Yukihiro Kimura / Zheng-Yu Wang-Otomo /
Abstract: is a moderately halophilic purple nonsulfur bacterium whose unique cell wall composition and phylogeny are distinct from those of all other purple phototrophs. Here we present a cryo-EM structure ... is a moderately halophilic purple nonsulfur bacterium whose unique cell wall composition and phylogeny are distinct from those of all other purple phototrophs. Here we present a cryo-EM structure and biochemical analysis of the light-harvesting 1-reaction center (LH1-RC) complex from at 2.29 Å resolution. The LH1 complex forms a closed ring structure with 16 αβ-polypeptides surrounding the RC and contains 16 phosphatidylglycerols regularly positioned between the β-polypeptides. Extensive interactions were observed between the C-terminal domains of LH1 α-and β-polypeptides and between the regularly arranged phosphatidylglycerols and β-polypeptides, supporting the hypothesis that LH1 C-terminal interactions define the post-translational truncation sites of αβ-polypeptides in phototrophic purple bacteria. Multiple insertions were identified in the membrane-extruded RC cytochrome- and H-subunits of . Insertions in the periplasm-exposed cytochrome subunit contain high proportions of Gly, Asp, and Glu, contributing to an overall negatively charged surface of this subunit. The cytoplasm-exposed H-subunit contained an unusually long 57-residue insert rich in Pro and Ala that was invisible in the cryo-EM density map, indicating its highly flexible nature. The extensive Pro-Ala repetitive motifs in this insertion points to a regulatory role in assemblies of the RC and LH1-RC complexes. The structural features of LH1-RC are also discussed in relation to differences in the physiological environment between the periplasmic and cytoplasmic sides of membranes in halophiles, necessary for maintaining cellular activities under the high ionic strength conditions of hypersaline environments.
History
DepositionJun 5, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_64946.png

Downloads & links

-
Map

FileDownload / File: emd_64946.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap including micelle density from the photosynthetic LH1-RC complex of the halophilic nonsulfur purple bacterium Rhodothalassium salexigens
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 380 pix.
= 311.6 Å		0.82 Å/pix.
x 380 pix.
= 311.6 Å		0.82 Å/pix.
x 380 pix.
= 311.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.18312213 - 0.34876728
Average (Standard dev.)0.00013683854 (±0.009773606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 311.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Even half map

Fileemd_64946_half_map_1.map
AnnotationEven half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Odd half map

Fileemd_64946_half_map_2.map
AnnotationOdd half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LH1-RC complex of Rhodothalassium salexigens

EntireName: LH1-RC complex of Rhodothalassium salexigens
Components
  • Complex: LH1-RC complex of Rhodothalassium salexigens

-
Supramolecule #1: LH1-RC complex of Rhodothalassium salexigens

SupramoleculeName: LH1-RC complex of Rhodothalassium salexigens / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Rhodothalassium salexigens DSM 2132 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5.9 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.03 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 377574
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229234
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more