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- EMDB-61212: Channel Rhodospin from Klebsormidium nitens (KnChR) -

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Basic information

Entry
Database: EMDB / ID: EMD-61212
TitleChannel Rhodospin from Klebsormidium nitens (KnChR)
Map data
Sample
  • Organelle or cellular component: 6-s-cis retinal
    • Protein or peptide: KnChR
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: RETINAL
  • Ligand: water
Keywordsblue-light absorbing / ELECTRON TRANSPORT
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / photoreceptor activity / phototransduction / plasma membrane / Uncharacterized protein
Function and homology information
Biological speciesKlebsormidium nitens (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsWang YZ / Akasaka H / Tanaka T / Sano FK / Shihoya W / Osamu N
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05777 Japan
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121002 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structure of a blue-shifted channelrhodopsin from Klebsormidium nitens
Authors: Wang YZ / Natsume K / Tanaka T / Hososhima S / Tashiro R / Sano FK / Akasaka H / Tsunoda SP / Shihoya W / Kandori H / Nureki O
History
DepositionAug 20, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61212.png

Downloads & links

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Map

FileDownload / File: emd_61212.map.gz / Format: CCP4 / Size: 75.1 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 270 pix.
= 224.1 Å		0.83 Å/pix.
x 270 pix.
= 224.1 Å		0.83 Å/pix.
x 270 pix.
= 224.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.07495572 - 0.22058843
Average (Standard dev.)0.00020252653 (±0.0067469357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 224.09999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61212_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61212_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 6-s-cis retinal

EntireName: 6-s-cis retinal
Components
  • Organelle or cellular component: 6-s-cis retinal
    • Protein or peptide: KnChR
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: RETINAL
  • Ligand: water

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Supramolecule #1: 6-s-cis retinal

SupramoleculeName: 6-s-cis retinal / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Klebsormidium nitens (plant)

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Macromolecule #1: KnChR

MacromoleculeName: KnChR / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsormidium nitens (plant)
Molecular weightTheoretical: 30.430072 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SCYVADFLGM HHESHEGALY SVYKSLEWGC FLISIGLFVF YLQQYRKKTA GWEVIYIAFI ESFKYIFEIF WPHNNPAQLN IYGVNKSVP WVRYMEWMIT CPVILMALSN ISGEEGEYTH RSMQLLATDQ GAILCAITAA ASEGAISAVF YAIGVCYGIC T FYFCLQIY ...String:
SCYVADFLGM HHESHEGALY SVYKSLEWGC FLISIGLFVF YLQQYRKKTA GWEVIYIAFI ESFKYIFEIF WPHNNPAQLN IYGVNKSVP WVRYMEWMIT CPVILMALSN ISGEEGEYTH RSMQLLATDQ GAILCAITAA ASEGAISAVF YAIGVCYGIC T FYFCLQIY IEAYFTLPET CHSAVKWMAV IFYAGWLCYP CFFLAGSEGW GNLSYEGSAI GHCIADLLSK NAWGVMHWWI RC QLEEYKH THNGQLPHYS LETRAKMR

UniProtKB: Uncharacterized protein

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

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

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

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Macromolecule #3: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 3 / Number of copies: 2 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 36 / 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 mMTris-HClTris Hydrochloride Acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 8554 / Average electron dose: 49.263 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3102701
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 164260
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: PHENIX
FSC plot (resolution estimation)

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