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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
Sample
  • Complex: predicted: CALHM1-like protein
    • Protein or peptide: Calcium homeostasis modulator protein
Keywordscomplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


ATP export / non-motile cilium / regulation of locomotion / monoatomic ion channel complex / monoatomic cation channel activity / voltage-gated calcium channel activity / calcium ion transmembrane transport / plasma membrane
Similarity search - Function
Calcium homeostasis modulator family / Calcium homeostasis modulator
Similarity search - Domain/homology
Calcium homeostasis modulator protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsYang WX / Wang YW
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.
History
DepositionJan 6, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing 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
  • Download
  • 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0938.png

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

Histogram

Histogram (log scale)
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
Components
  • Complex: predicted: CALHM1-like protein
    • Protein or peptide: Calcium homeostasis modulator protein

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Supramolecule #1: predicted: CALHM1-like protein

SupramoleculeName: predicted: CALHM1-like protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Calcium homeostasis modulator protein

MacromoleculeName: Calcium homeostasis modulator protein / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 37.308633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTTSINSVVT VFQNVFTNHG STLLNGILIA TTVGGQSLVR KLTFSCPCAY PLNIYHSLVF MFGPTAALLL IGITVNSTTW KLAHGFFFR VRDTRHSWKT TCVSWIEVLI QSSVAPIAWL FVVFLDGGYY RCYRSHEFCL ISDAILCKNS TILNSYASTS S FNKISDNG ...String:
MTTSINSVVT VFQNVFTNHG STLLNGILIA TTVGGQSLVR KLTFSCPCAY PLNIYHSLVF MFGPTAALLL IGITVNSTTW KLAHGFFFR VRDTRHSWKT TCVSWIEVLI QSSVAPIAWL FVVFLDGGYY RCYRSHEFCL ISDAILCKNS TILNSYASTS S FNKISDNG KYCPPCICVP NPTDASYLEA ESQIYAWGLL LFSGVAAFLV ITCNRMCDKY TLVQRQYVET YKNVETQKFD AV AKEHASQ LAEHNARAFF GQKDWTKRDW DWVSGIPEVN NPLFARLRLI AAEKTQQTMY TPLQLWNDNK GYRIPQPDLQ LTQ IIVDET KED

UniProtKB: Calcium homeostasis modulator protein

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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