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- EMDB-35143: Cryo-EM structure of the zeaxanthin-bound kin4B8 -

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Basic information

Entry
Database: EMDB / ID: EMD-35143
TitleCryo-EM structure of the zeaxanthin-bound kin4B8
Map data
Sample
  • Organelle or cellular component: Kin4B8
    • Protein or peptide: Xanthorhodopsin
  • Ligand: RETINAL
  • Ligand: Zeaxanthin
  • Ligand: water
KeywordsRhodopsin / Cryo-EM / anntena / PROTON TRANSPORT
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / membrane
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
Biological speciesuncultured Bdellovibrionales bacterium (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsMurakoshi S / Chazan A / Shihoya W / Beja O / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nature / Year: 2023
Title: Phototrophy by antenna-containing rhodopsin pumps in aquatic environments.
Authors: Ariel Chazan / Ishita Das / Takayoshi Fujiwara / Shunya Murakoshi / Andrey Rozenberg / Ana Molina-Márquez / Fumiya K Sano / Tatsuki Tanaka / Patricia Gómez-Villegas / Shirley Larom / Alina ...Authors: Ariel Chazan / Ishita Das / Takayoshi Fujiwara / Shunya Murakoshi / Andrey Rozenberg / Ana Molina-Márquez / Fumiya K Sano / Tatsuki Tanaka / Patricia Gómez-Villegas / Shirley Larom / Alina Pushkarev / Partha Malakar / Masumi Hasegawa / Yuya Tsukamoto / Tomohiro Ishizuka / Masae Konno / Takashi Nagata / Yosuke Mizuno / Kota Katayama / Rei Abe-Yoshizumi / Sanford Ruhman / Keiichi Inoue / Hideki Kandori / Rosa León / Wataru Shihoya / Susumu Yoshizawa / Mordechai Sheves / Osamu Nureki / Oded Béjà /
Abstract: Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium and a ...Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium and a terrestrial cyanobacterium. Attempts to find carotenoids that bind and transfer energy to abundant rhodopsin proton pumps from marine photoheterotrophs have thus far failed. Here we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins using functional metagenomics combined with chromophore extraction from the environment. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet- or blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas may have a substantial effect on rhodopsin phototrophy in the world's lakes, seas and oceans. However, the functional implications of our findings are yet to be discovered.
History
DepositionJan 15, 2023-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35143.png

Downloads & links

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Map

FileDownload / File: emd_35143.map.gz / Format: CCP4 / Size: 7.2 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 108 pix.
= 89.64 Å		0.83 Å/pix.
x 134 pix.
= 111.22 Å		0.83 Å/pix.
x 130 pix.
= 107.9 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-7.4783454 - 11.259563999999999
Average (Standard dev.)0.000655529 (±0.93943554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin114113122
Dimensions134130108
Spacing130134108
CellA: 107.9 Å / B: 111.22 Å / C: 89.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35143_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_35143_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35143_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Kin4B8

EntireName: Kin4B8
Components
  • Organelle or cellular component: Kin4B8
    • Protein or peptide: Xanthorhodopsin
  • Ligand: RETINAL
  • Ligand: Zeaxanthin
  • Ligand: water

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Supramolecule #1: Kin4B8

SupramoleculeName: Kin4B8 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: uncultured Bdellovibrionales bacterium (environmental samples)

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Macromolecule #1: Xanthorhodopsin

MacromoleculeName: Xanthorhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: uncultured Bdellovibrionales bacterium (environmental samples)
Molecular weightTheoretical: 28.745842 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSATTLTLQQ FSTVYNMLSF AVASMLGAFA FFVMGRKIVG PKYRLALVVS SLVVLIAGYH YWRIMGSWTA AYALKDGMYV PTGEPFNDA YRYVDWLLTV PLLLTELVLV MKLKKESGSV LAKLILAAIA MIALGYPGEI SNPESQAGAR LMWGVLSTVP F LYILYVLW ...String:
MSATTLTLQQ FSTVYNMLSF AVASMLGAFA FFVMGRKIVG PKYRLALVVS SLVVLIAGYH YWRIMGSWTA AYALKDGMYV PTGEPFNDA YRYVDWLLTV PLLLTELVLV MKLKKESGSV LAKLILAAIA MIALGYPGEI SNPESQAGAR LMWGVLSTVP F LYILYVLW VRLGDAIGEH PAKVQVLLKN TRYLILLTWG FYPIVYAMGS YGWLGGAGSV VAVQVGYSIA DVTAKALYGV MI FAIAYAK SEADGSLPAH HHHHH

UniProtKB: Xanthorhodopsin

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Macromolecule #2: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 2 / Number of copies: 1 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #3: Zeaxanthin

MacromoleculeName: Zeaxanthin / type: ligand / ID: 3 / Number of copies: 1 / Formula: K3I
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-K3I:
Zeaxanthin

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 33 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC4H11NO3tris hydroxymethyl aminomethane

Details: 150 mM NaCl, 20 mM Tris-HCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Details: Vitrification carried out in ethane atmosphere..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.14 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4337540
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.0)

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