[English] 日本語
Yorodumi
- EMDB-53520: Cryo-EM structure of the light-driven proton pump PsPR in deterge... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53520
TitleCryo-EM structure of the light-driven proton pump PsPR in detergent micelle
Map dataSharpened map used for manual and automatic model refinement
Sample
  • Complex: proteorhodopsin
    • Protein or peptide: microbial rhodopsin
  • Ligand: EICOSANE
  • Ligand: RETINAL
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water
Keywordsproton transport / retinal / bioenergetics / proteorhodopsin / microbial rhodopsin / MEMBRANE PROTEIN
Biological speciesCandidatus Pseudothioglobus sp. (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsKovalev K / Stetsenko A / Guskov A
Funding support Netherlands, Germany, 3 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
Netherlands Organisation for Scientific Research (NWO)OCENW.KLEIN.141 Netherlands
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND847543 Germany
CitationJournal: Structure / Year: 2025
Title: Structural basis for no retinal binding in flotillin-associated rhodopsins.
Authors: Kirill Kovalev / Artem Stetsenko / Florian Trunk / Egor Marin / Jose M Haro-Moreno / Gerrit H U Lamm / Alexey Alekseev / Francisco Rodriguez-Valera / Thomas R Schneider / Josef Wachtveitl / Albert Guskov /
Abstract: Rhodopsins are light-sensitive membrane proteins capturing solar energy via a retinal cofactor covalently attached to a lysine residue. Several groups of rhodopsins lack the conserved lysine and ...Rhodopsins are light-sensitive membrane proteins capturing solar energy via a retinal cofactor covalently attached to a lysine residue. Several groups of rhodopsins lack the conserved lysine and showed no retinal binding. Recently, flotillin-associated rhodopsins (FArhodopsins or FARs) were identified and suggested to lack the retinal-binding pocket despite preserving the lysine residue in many members of the group. Here, we present cryoelectron microscopic (cryo-EM) structures of paralog FArhodopsin and proteorhodopsin from marine bacterium Pseudothioglobus, both forming pentamers similar to those of other microbial rhodopsins. We demonstrate no binding of retinal to the FArhodopsin despite preservation of the lysine residue and overall similarity of the protein fold and internal organization to those of the retinal-binding paralog. Mutational analysis confirmed that two amino acids, H84 and E120, prevent retinal binding within the FArhodopsin. Our work provides insights into the natural retinal loss in microbial rhodopsins and might contribute to the further understanding of FArhodopsins.
History
DepositionApr 29, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53520.png

Downloads & links

-
Map

FileDownload / File: emd_53520.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map used for manual and automatic model refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 280 pix.
= 234.08 Å		0.84 Å/pix.
x 280 pix.
= 234.08 Å		0.84 Å/pix.
x 280 pix.
= 234.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.137
Minimum - Maximum-0.6477279 - 0.8468044
Average (Standard dev.)0.0004860929 (±0.023889577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 234.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Non-sharpened map used for validation against coordinates

Fileemd_53520_additional_1.map
AnnotationNon-sharpened map used for validation against coordinates
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_53520_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_53520_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : proteorhodopsin

EntireName: proteorhodopsin
Components
  • Complex: proteorhodopsin
    • Protein or peptide: microbial rhodopsin
  • Ligand: EICOSANE
  • Ligand: RETINAL
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water

-
Supramolecule #1: proteorhodopsin

SupramoleculeName: proteorhodopsin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Candidatus Pseudothioglobus sp. (bacteria)
Molecular weightTheoretical: 150 KDa

-
Macromolecule #1: microbial rhodopsin

MacromoleculeName: microbial rhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Pseudothioglobus sp. (bacteria)
Molecular weightTheoretical: 26.467082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLQAGDFVGV SFWLVSVAMV AATVFFFYEG MSVKKEWKLS MTIAGLVTLV AAIHYYYMRD YWVASVLAGS PDSPIVYRYI DWLITVPLL MIEFFIILKA VGASISTNSF WRLLVGTLVM LIGGFAGEAM LISASLGFII GMVGWAIIIW EIFGGEASKA A DANAGVKS ...String:
MLQAGDFVGV SFWLVSVAMV AATVFFFYEG MSVKKEWKLS MTIAGLVTLV AAIHYYYMRD YWVASVLAGS PDSPIVYRYI DWLITVPLL MIEFFIILKA VGASISTNSF WRLLVGTLVM LIGGFAGEAM LISASLGFII GMVGWAIIIW EIFGGEASKA A DANAGVKS AFNALRLIVL VGWAIYPLGY IFGYMMGSVD SGSLNIIYNL ADFVNKILFG LIIWNVAVRE SSDALEHHHH HH

-
Macromolecule #2: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 2 / Number of copies: 30 / Formula: LFA
Molecular weightTheoretical: 282.547 Da
Chemical component information

ChemComp-LFA:
EICOSANE

-
Macromolecule #3: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 3 / Number of copies: 5 / Formula: RET
Source (natural)Organism: Candidatus Pseudothioglobus sp. (bacteria)
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

-
Macromolecule #4: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 4 / Number of copies: 5 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 105 / 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

Concentration8 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 5 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time 4-6 second, force 0.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 497291
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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