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- EMDB-16313: The structure of the rod CNG channel bound to calmodulin -

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Basic information

Entry
Database: EMDB / ID: EMD-16313
TitleThe structure of the rod CNG channel bound to calmodulin
Map data
Sample
  • Complex: Native CNG channel from retinal rods
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.66 Å
AuthorsMarino J
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation19082 Switzerland
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structural basis of calmodulin modulation of the rod cyclic nucleotide-gated channel.
Authors: Diane C A Barret / Dina Schuster / Matthew J Rodrigues / Alexander Leitner / Paola Picotti / Gebhard F X Schertler / U Benjamin Kaupp / Volodymyr M Korkhov / Jacopo Marino /
Abstract: Calmodulin (CaM) regulates many ion channels to control calcium entry into cells, and mutations that alter this interaction are linked to fatal diseases. The structural basis of CaM regulation ...Calmodulin (CaM) regulates many ion channels to control calcium entry into cells, and mutations that alter this interaction are linked to fatal diseases. The structural basis of CaM regulation remains largely unexplored. In retinal photoreceptors, CaM binds to the CNGB subunit of cyclic nucleotide-gated (CNG) channels and, thereby, adjusts the channel's Cyclic guanosine monophosphate (cGMP) sensitivity in response to changes in ambient light conditions. Here, we provide the structural characterization for CaM regulation of a CNG channel by using a combination of single-particle cryo-electron microscopy and structural proteomics. CaM connects the CNGA and CNGB subunits, resulting in structural changes both in the cytosolic and transmembrane regions of the channel. Cross-linking and limited proteolysis-coupled mass spectrometry mapped the conformational changes induced by CaM in vitro and in the native membrane. We propose that CaM is a constitutive subunit of the rod channel to ensure high sensitivity in dim light. Our mass spectrometry-based approach is generally relevant for studying the effect of CaM on ion channels in tissues of medical interest, where only minute quantities are available.
History
DepositionDec 8, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16313.png

Downloads & links

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Map

FileDownload / File: emd_16313.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 320 pix.
= 326.4 Å		1.02 Å/pix.
x 320 pix.
= 326.4 Å		1.02 Å/pix.
x 320 pix.
= 326.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.101
Minimum - Maximum-0.21384448 - 0.5894395
Average (Standard dev.)5.0765753e-05 (±0.009733446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 326.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16313_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_16313_half_map_2.map
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Sample components

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Entire : Native CNG channel from retinal rods

EntireName: Native CNG channel from retinal rods
Components
  • Complex: Native CNG channel from retinal rods

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Supramolecule #1: Native CNG channel from retinal rods

SupramoleculeName: Native CNG channel from retinal rods / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 410 KDa

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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

Concentration0.3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 101769
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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