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- PDB-8i2z: Cryo-EM structure of the zeaxanthin-bound kin4B8 -

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Basic information

Entry
Database: PDB / ID: 8i2z
TitleCryo-EM structure of the zeaxanthin-bound kin4B8
ComponentsXanthorhodopsin
KeywordsPROTON TRANSPORT / Rhodopsin / Cryo-EM / anntena
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
Zeaxanthin / RETINAL / Xanthorhodopsin
Similarity search - Component
Biological speciesuncultured Bdellovibrionales bacterium (environmental samples)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsMurakoshi, S. / Chazan, A. / Shihoya, W. / Beja, O. / Nureki, O.
Funding support Japan, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / refine
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification ..._em_admin.last_update / _pdbx_entry_details.has_protein_modification / _refine.ls_d_res_high / _refine.ls_d_res_low
Revision 1.3Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xanthorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5993
Polymers28,7461
Non-polymers8532
Water59433
1
A: Xanthorhodopsin
hetero molecules
x 5


Theoretical massNumber of molelcules
Total (without water)147,99615
Polymers143,7295
Non-polymers4,26710
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C5 (5 fold cyclic))

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Components

#1: Protein Xanthorhodopsin / Kin4B8


Mass: 28745.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured Bdellovibrionales bacterium (environmental samples)
Gene: tmp_000014 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A977XLG0
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K3I / Zeaxanthin / zeaxanthin


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Kin4B8 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: uncultured Bdellovibrionales bacterium (environmental samples)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 150 mM NaCl, 20 mM Tris-HCl
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMtris hydroxymethyl aminomethaneC4H11NO31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Vitrification carried out in ethane atmosphere.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50.14 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategory
4RELION3.1CTF correction
8PHENIXmodel refinement
10cryoSPARC2initial Euler assignment
11cryoSPARC2final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4337540 / Symmetry type: POINT
RefinementResolution: 2.3→2.3 Å / Cor.coef. Fo:Fc: 0.899 / SU B: 3.934 / SU ML: 0.087 / ESU R: 0.05
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.27887 --
obs0.27887 259007 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 86.425 Å2
Refinement stepCycle: 1 / Total: 2050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.0132071
ELECTRON MICROSCOPYr_bond_other_d0.0310.0172056
ELECTRON MICROSCOPYr_angle_refined_deg1.3321.6342827
ELECTRON MICROSCOPYr_angle_other_deg1.6131.5654689
ELECTRON MICROSCOPYr_dihedral_angle_1_deg3.9735253
ELECTRON MICROSCOPYr_dihedral_angle_2_deg28.52918.24797
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.09615318
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.128157
ELECTRON MICROSCOPYr_chiral_restr0.0840.2261
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.022313
ELECTRON MICROSCOPYr_gen_planes_other0.0020.02484
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it7.8528.4281015
ELECTRON MICROSCOPYr_mcbond_other7.8378.421014
ELECTRON MICROSCOPYr_mcangle_it9.62612.6931267
ELECTRON MICROSCOPYr_mcangle_other9.6312.7011268
ELECTRON MICROSCOPYr_scbond_it10.0439.6471056
ELECTRON MICROSCOPYr_scbond_other10.0389.6461057
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other14.14914.071561
ELECTRON MICROSCOPYr_long_range_B_refined17.8898919
ELECTRON MICROSCOPYr_long_range_B_other17.8848903
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.571 19094 -
obs--100 %

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