[English] 日本語
Yorodumi
- EMDB-61688: Cryo-EM structure of the light-driven chloride ion-pumping rhodop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61688
TitleCryo-EM structure of the light-driven chloride ion-pumping rhodopsin, NM-R3
Map data
Sample
  • Complex: NM-R3
    • Protein or peptide: Chloride pumping rhodopsin
  • Ligand: RETINAL
  • Ligand: CHLORIDE ION
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: DODECANE
  • Ligand: HEXADECANE
  • Ligand: Octadecane
  • Ligand: TETRADECANE
  • Ligand: water
Keywordschloride ion-pumping rhodopsin RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin / MEMBRANE PROTEIN
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / photoreceptor activity / phototransduction / membrane / Chloride pumping rhodopsin
Function and homology information
Biological speciesNonlabens marinus S1-08 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsHosaka T / Shirouzu M
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Microbiol / Year: 2025
Title: Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota.
Authors: Takayoshi Fujiwara / Toshiaki Hosaka / Masumi Hasegawa-Takano / Yosuke Nishimura / Kento Tominaga / Kaho Mori / Satoshi Nishino / Yuno Takahashi / Tomomi Uchikubo-Kamo / Kazuharu Hanada / ...Authors: Takayoshi Fujiwara / Toshiaki Hosaka / Masumi Hasegawa-Takano / Yosuke Nishimura / Kento Tominaga / Kaho Mori / Satoshi Nishino / Yuno Takahashi / Tomomi Uchikubo-Kamo / Kazuharu Hanada / Takashi Maoka / Shinichi Takaichi / Keiichi Inoue / Mikako Shirouzu / Susumu Yoshizawa /
Abstract: Microbial rhodopsins are photoreceptor proteins widely distributed in marine microorganisms that harness light energy and support marine ecosystems. While retinal is typically the sole chromophore in ...Microbial rhodopsins are photoreceptor proteins widely distributed in marine microorganisms that harness light energy and support marine ecosystems. While retinal is typically the sole chromophore in microbial rhodopsins, some proteorhodopsins, which are proton-pumping rhodopsins abundant in the ocean, use carotenoid antennae to transfer light energy to retinal. However, the mechanism by which carotenoids enhance rhodopsin functions remains unclear. Here, using the marine Bacteroidota isolate Nonlabens marinus S1-08, we reconstituted complexes of rhodopsins with the carotenoid myxol and detected energy transfer to retinal in both proteorhodopsin and chloride ion-pumping rhodopsin. Carotenoid binding facilitated light harvesting and accelerated the photocycle, thereby improving the light utilization efficiency of proteorhodopsin. Cryogenic electron microscopy structural analysis further revealed the molecular architecture of the carotenoid-rhodopsin complexes. The ability to bind carotenoids is conserved in rhodopsins of the marine-dominant phylum Bacteroidota, which are widely transcribed in the photic zone. These findings reveal how carotenoids enhance rhodopsin functions in marine Bacteroidota.
History
DepositionSep 25, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_61688.png

Downloads & links

-
Map

FileDownload / File: emd_61688.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 200 pix.
= 165.7 Å		0.83 Å/pix.
x 200 pix.
= 165.7 Å		0.83 Å/pix.
x 200 pix.
= 165.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.031
Minimum - Maximum-0.033433408 - 0.093846165
Average (Standard dev.)0.0012689352 (±0.006680538)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 165.7 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_61688_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61688_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61688_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : NM-R3

EntireName: NM-R3
Components
  • Complex: NM-R3
    • Protein or peptide: Chloride pumping rhodopsin
  • Ligand: RETINAL
  • Ligand: CHLORIDE ION
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: DODECANE
  • Ligand: HEXADECANE
  • Ligand: Octadecane
  • Ligand: TETRADECANE
  • Ligand: water

+
Supramolecule #1: NM-R3

SupramoleculeName: NM-R3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)

+
Macromolecule #1: Chloride pumping rhodopsin

MacromoleculeName: Chloride pumping rhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Nonlabens marinus S1-08 (bacteria)
Molecular weightTheoretical: 30.710936 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSSGSSGMKN IESLFDYSAG QFEFIDHLLT MGVGVHFAAL IFFLVVSQFV APKYRIATAL SCIVMVSAGL ILNSQAVMWT DAYAYVDGS YQLQDLTFSN GYRYVNWMAT IPCLLLQLLI VLNLKGKELF STATWLILAA WGMIITGYVG QLYEVDDIAQ L MIWGAVST ...String:
GSSGSSGMKN IESLFDYSAG QFEFIDHLLT MGVGVHFAAL IFFLVVSQFV APKYRIATAL SCIVMVSAGL ILNSQAVMWT DAYAYVDGS YQLQDLTFSN GYRYVNWMAT IPCLLLQLLI VLNLKGKELF STATWLILAA WGMIITGYVG QLYEVDDIAQ L MIWGAVST AFFVVMNWIV GTKIFKNRAT MLGGTDSTIT KVFWLMMFAW TLYPIAYLVP AFMNNADGVV LRQLLFTIAD IS SKVIYGL MITYIAIQQS AAAGYVPAQQ ALGRIGMDSK AA

UniProtKB: Chloride pumping rhodopsin

+
Macromolecule #2: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 2 / Number of copies: 5 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

+
Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 10 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #4: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 4 / Number of copies: 5 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

+
Macromolecule #5: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 5 / Number of copies: 5 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

+
Macromolecule #6: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 6 / Number of copies: 2 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

+
Macromolecule #7: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 7 / Number of copies: 6 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

+
Macromolecule #8: Octadecane

MacromoleculeName: Octadecane / type: ligand / ID: 8 / Number of copies: 2 / Formula: 8K6
Molecular weightTheoretical: 254.494 Da
Chemical component information

ChemComp-8K6:
Octadecane

+
Macromolecule #9: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 9 / Number of copies: 2 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

+
Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 150 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.534 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5b2n

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2081189
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