[English] 日本語
Yorodumi
- EMDB-40062: Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40062
TitleKalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) embedded in peptidisc
Map data
Sample
  • Complex: Kalium channelrhodopsin 1 trimer reconstituted into nanodiscs
    • Protein or peptide: Kalium Channelrhodopsin 1
  • Ligand: RETINAL
  • Ligand: SODIUM ION
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: water
KeywordsRetinal Protein / Channelrhodopsin / Cation channel / Peptidisc / Optogenetics / TRANSPORT PROTEIN
Biological speciesHyphochytrium catenoides (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsMorizumi T / Kim K / Li H / Spudich JL / Ernst OP
Funding support Canada, 3 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04397 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06862 Canada
Canadian Institutes of Health Research (CIHR)PJT-159464 Canada
CitationJournal: Nat Commun / Year: 2023
Title: Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K and Na selectivities.
Authors: Takefumi Morizumi / Kyumhyuk Kim / Hai Li / Elena G Govorunova / Oleg A Sineshchekov / Yumei Wang / Lei Zheng / Éva Bertalan / Ana-Nicoleta Bondar / Azam Askari / Leonid S Brown / John L ...Authors: Takefumi Morizumi / Kyumhyuk Kim / Hai Li / Elena G Govorunova / Oleg A Sineshchekov / Yumei Wang / Lei Zheng / Éva Bertalan / Ana-Nicoleta Bondar / Azam Askari / Leonid S Brown / John L Spudich / Oliver P Ernst /
Abstract: Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is a light-gated channel used for optogenetic silencing of mammalian neurons. It selects K over Na in the absence of the canonical ...Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is a light-gated channel used for optogenetic silencing of mammalian neurons. It selects K over Na in the absence of the canonical tetrameric K selectivity filter found universally in voltage- and ligand-gated channels. The genome of H. catenoides also encodes a highly homologous cation channelrhodopsin (HcCCR), a Na channel with >100-fold larger Na to K permeability ratio. Here, we use cryo-electron microscopy to determine atomic structures of these two channels embedded in peptidiscs to elucidate structural foundations of their dramatically different cation selectivity. Together with structure-guided mutagenesis, we show that K versus Na selectivity is determined at two distinct sites on the putative ion conduction pathway: in a patch of critical residues in the intracellular segment (Leu69/Phe69, Ile73/Ser73 and Asp116) and within a cluster of aromatic residues in the extracellular segment (primarily, Trp102 and Tyr222). The two filters are on the opposite sides of the photoactive site involved in channel gating.
History
DepositionMar 13, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40062.png

Downloads & links

-
Map

FileDownload / File: emd_40062.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-5.782335 - 8.934065
Average (Standard dev.)-0.00028212828 (±0.1791478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_40062_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_40062_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Kalium channelrhodopsin 1 trimer reconstituted into nanodiscs

EntireName: Kalium channelrhodopsin 1 trimer reconstituted into nanodiscs
Components
  • Complex: Kalium channelrhodopsin 1 trimer reconstituted into nanodiscs
    • Protein or peptide: Kalium Channelrhodopsin 1
  • Ligand: RETINAL
  • Ligand: SODIUM ION
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: water

-
Supramolecule #1: Kalium channelrhodopsin 1 trimer reconstituted into nanodiscs

SupramoleculeName: Kalium channelrhodopsin 1 trimer reconstituted into nanodiscs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Hyphochytrium catenoides (eukaryote)
Molecular weightTheoretical: 30.49385 KDa

-
Macromolecule #1: Kalium Channelrhodopsin 1

MacromoleculeName: Kalium Channelrhodopsin 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hyphochytrium catenoides (eukaryote)
Molecular weightTheoretical: 30.515744 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MPFYDSRPPE GWPKGSINDM DYPLLGSICA VCCVFVAGSG IWMLYRLDLG MGYSCKPYKS GRAPEVNSLS GIICLLCGTM YAAKSFDFF DGGGTPFSLN WYWYLDYVFT CPLLILDFAF TLDLPHKIRY FFAVFLTLWC GVAAFVTPSA YRFAYYALGC C WFTPFALS ...String:
MPFYDSRPPE GWPKGSINDM DYPLLGSICA VCCVFVAGSG IWMLYRLDLG MGYSCKPYKS GRAPEVNSLS GIICLLCGTM YAAKSFDFF DGGGTPFSLN WYWYLDYVFT CPLLILDFAF TLDLPHKIRY FFAVFLTLWC GVAAFVTPSA YRFAYYALGC C WFTPFALS LMRHVKERYL VYPPKCQRWL FWACVIFFGF WPMFPILFIF SWLGTGHISQ QAFYIIHAFL DLTCKSIFGI LM TVFRLEL EEHTEVQGLP LNEPETLS

-
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

-
Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

-
Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 3 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Macromolecule #5: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 5 / Number of copies: 5 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 15 / 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

Concentration0.35 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMC8H18N2O4SHEPES
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was kept in the dark prior to freezing.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 12104 / Average electron dose: 40.0 e/Å2
Details: Images collected in movie mode, 30 fractions per movie, Falcon 4i detector
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsFalcon 4i detector. Images were reference corrected.
Particle selectionNumber selected: 5692131
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 297015
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 124187 / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 158.5 / Target criteria: Cross correlation coefficent
Output model

PDB-8gi8:
Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) embedded in peptidisc

+
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