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- PDB-9j7w: Channel Rhodospin from Klebsormidium nitens (KnChR) -

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Basic information

Entry
Database: PDB / ID: 9j7w
TitleChannel Rhodospin from Klebsormidium nitens (KnChR)
ComponentsKnChR
KeywordsELECTRON TRANSPORT / blue-light absorbing
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / photoreceptor activity / phototransduction / plasma membrane / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / RETINAL / Uncharacterized protein
Function and homology information
Biological speciesKlebsormidium nitens (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsWang, Y.Z. / Akasaka, H. / Tanaka, T. / Sano, F.K. / Shihoya, W. / Nureki, O.
Funding support Japan, 3items
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, Y.Z. / Natsume, K. / Tanaka, T. / Hososhima, S. / Tashiro, R. / Sano, F.K. / Akasaka, H. / Tsunoda, S.P. / Shihoya, W. / Kandori, H. / Nureki, O.
History
DepositionAug 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KnChR
C: KnChR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0096
Polymers60,8602
Non-polymers2,1494
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein KnChR


Mass: 30430.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsormidium nitens (plant) / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A1Y1HT90
#2: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 6-s-cis retinal / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsormidium nitens (plant)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMTris Hydrochloride AcidTris-HCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 49.263 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 8554
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3particle selection
4cryoSPARC3.3CTF correction
9cryoSPARC3.3initial Euler assignment
10PHENIXfinal Euler assignment
11cryoSPARC3.3classification
12Coot3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3102701
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164260 / Symmetry type: POINT

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