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- PDB-6lom: Structure of CLHM1 from Caenorhabditis Elegans -

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Basic information

Entry
Database: PDB / ID: 6lom
TitleStructure of CLHM1 from Caenorhabditis Elegans
ComponentsCalcium homeostasis modulator protein
KeywordsMEMBRANE PROTEIN / complex
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsYang, W.X. / Wang, Y.W. / Zhang, X.C.
Funding support China, 1items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Calcium homeostasis modulator protein
B: Calcium homeostasis modulator protein
C: Calcium homeostasis modulator protein
D: Calcium homeostasis modulator protein
E: Calcium homeostasis modulator protein
F: Calcium homeostasis modulator protein
G: Calcium homeostasis modulator protein
H: Calcium homeostasis modulator protein
I: Calcium homeostasis modulator protein
J: Calcium homeostasis modulator protein
K: Calcium homeostasis modulator protein
L: Calcium homeostasis modulator protein
M: Calcium homeostasis modulator protein
N: Calcium homeostasis modulator protein
O: Calcium homeostasis modulator protein
P: Calcium homeostasis modulator protein
Q: Calcium homeostasis modulator protein
R: Calcium homeostasis modulator protein
S: Calcium homeostasis modulator protein
T: Calcium homeostasis modulator protein


Theoretical massNumber of molelcules
Total (without water)746,17320
Polymers746,17320
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area114780 Å2
ΔGint-1026 kcal/mol
Surface area282170 Å2

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Components

#1: Protein
Calcium homeostasis modulator protein / CALHM1-like protein


Mass: 37308.633 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: clhm-1, C44B7.4 / Production host: Homo sapiens (human) / References: UniProt: Q18593
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: predicted: CALHM1-like protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49000 / Symmetry type: POINT

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