8GI8

Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) embedded in peptidisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K + and Na + selectivities.

Morizumi, T.Kim, K.Li, H.Govorunova, E.G.Sineshchekov, O.A.Wang, Y.Zheng, L.Bertalan, E.Bondar, A.N.Askari, A.Brown, L.S.Spudich, J.L.Ernst, O.P.

(2023) Nat Commun 14: 4365-4365

  • DOI: https://doi.org/10.1038/s41467-023-40041-2
  • Primary Citation of Related Structures:  
    8GI8, 8GI9

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, ON, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kalium Channelrhodopsin 1265Hyphochytrium catenoidesMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEE
Query on PEE

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
RET
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.1
MODEL REFINEMENTPHENIX1.20
MODEL REFINEMENTCoot0.8.9.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2018-04397
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2017-06862
Canadian Institutes of Health Research (CIHR)CanadaPJT-159464

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references