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- EMDB-0938: Structure of CLHM1 from Caenorhabditis Elegans -

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Basic information

Entry
Database: EMDB / ID: EMD-0938
TitleStructure of CLHM1 from Caenorhabditis Elegans
Map data
Samplepredicted: CALHM1-like protein:
Calcium homeostasis modulator protein
Function / homology
Function and homology information


regulation of locomotion / non-motile cilium / voltage-gated calcium channel activity / regulation of ion transmembrane transport / cation channel activity / calcium ion transmembrane transport / integral component of plasma membrane / plasma membrane
Calcium homeostasis modulator family
Calcium homeostasis modulator protein
Biological speciesCaenorhabditis elegans (roundworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsYang WX / Wang YW / Zhang XC
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Protein Sci. / Year: 2020
Title: Cryo-electron microscopy structure of CLHM1 ion channel from Caenorhabditis elegans.
Authors: Weixin Yang / Youwang Wang / Jianli Guo / Lingli He / Ye Zhou / Hui Zheng / Zhenfeng Liu / Ping Zhu / Xuejun C Zhang /
Abstract: Calcium homeostasis modulators (CALHMs/CLHMs) comprise a family of pore-forming protein complexes assembling into voltage-gated, Ca -sensitive, nonselective channels. These complexes contain an ion- ...Calcium homeostasis modulators (CALHMs/CLHMs) comprise a family of pore-forming protein complexes assembling into voltage-gated, Ca -sensitive, nonselective channels. These complexes contain an ion-conduction pore sufficiently wide to permit the passing of ATP molecules serving as neurotransmitters. While their function and structure information is accumulating, the precise mechanisms of these channel complexes remain to be full understood. Here, we present the structure of the Caenorhabditis elegans CLHM1 channel in its open state solved through single-particle cryo-electron microscopy at 3.7-Å resolution. The transmembrane region of the channel structure of the dominant class shows an assembly of 10-fold rotational symmetry in one layer, and its cytoplasmic region is involved in additional twofold symmetrical packing in a tail-to-tail manner. Furthermore, we identified a series of amino acid residues critical for the regulation of CeCLHM1 channel using functional assays, electrophysiological analyses as well as structural-based analysis. Our structure and function analyses provide new insights into the mechanisms of CALHM channels.
Validation ReportPDB-ID: 6lom

SummaryFull reportAbout validation report
History
DepositionJan 6, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.26
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.26
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lom
  • Surface level: 0.26
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0938.map.gz / Format: CCP4 / Size: 103 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 Å/pix.
x 300 pix.
= 300. Å
1 Å/pix.
x 300 pix.
= 300. Å
1 Å/pix.
x 300 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.26 / Movie #1: 0.26
Minimum - Maximum-1.180537 - 1.6566176
Average (Standard dev.)0.014908522 (±0.071105346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-1.1811.6570.015

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Supplemental data

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Sample components

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Entire predicted: CALHM1-like protein

EntireName: predicted: CALHM1-like protein / Number of components: 2

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Component #1: protein, predicted: CALHM1-like protein

ProteinName: predicted: CALHM1-like protein / Recombinant expression: No
SourceSpecies: Caenorhabditis elegans (roundworm)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Calcium homeostasis modulator protein

ProteinName: Calcium homeostasis modulator protein / Number of Copies: 20 / Recombinant expression: No
MassTheoretical: 37.308633 kDa
SourceSpecies: Caenorhabditis elegans (roundworm)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 49000
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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