6LMV | pdb_00006lmv

Cryo-EM structure of the C. elegans CLHM-1

• PDB DOI: https://doi.org/10.2210/pdb6LMV/pdb
• EM Map EMD-0921: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-12-26 Released: 2020-07-29 
• Deposition Author(s): Demura, K., Kusakizako, T., Shihoya, W., Hiraizumi, M., Shimada, H., Yamashita, K., Nishizawa, T., Nureki, O.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures of calcium homeostasis modulator channels in diverse oligomeric assemblies.

Demura, K., Kusakizako, T., Shihoya, W., Hiraizumi, M., Nomura, K., Shimada, H., Yamashita, K., Nishizawa, T., Taruno, A., Nureki, O.

(2020) Sci Adv 6: eaba8105-eaba8105

• PubMed: 32832629 
• DOI: https://doi.org/10.1126/sciadv.aba8105
• Primary Citation Related Structures: 
  6LMT, 6LMU, 6LMV, 6LMW, 6LMX


• PubMed Abstract: 
  

  Calcium homeostasis modulator (CALHM) family proteins are Ca ²⁺ -regulated adenosine triphosphate (ATP)-release channels involved in neural functions including neurotransmission in gustation. Here, we present the cryo-electron microscopy (EM) structures of killifish CALHM1, human CALHM2, and Caenorhabditis elegans CLHM-1 at resolutions of 2.66, 3.4, and 3.6 Å, respectively. The CALHM1 octamer structure reveals that the N-terminal helix forms the constriction site at the channel pore in the open state and modulates the ATP conductance. The CALHM2 undecamer and CLHM-1 nonamer structures show the different oligomeric stoichiometries among CALHM homologs. We further report the cryo-EM structures of the chimeric construct, revealing that the intersubunit interactions at the transmembrane domain (TMD) and the TMD-intracellular domain linker define the oligomeric stoichiometry. These findings advance our understanding of the ATP conduction and oligomerization mechanisms of CALHM channels.

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Organizational Affiliation: 
• Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Discovery Technology Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida, Aoba-ku, Yokohama 227-0033, Japan.
Department of Molecular Cell Physiology, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Japan.
RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C9  (Explore in 3D)
Global Stoichiometry: Homo 9-mer - A9 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 345.11 kDa 
• Atom Count: 17,766 
• Modeled Residue Count: 2,223 
• Deposited Residue Count: 3,033 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium homeostasis modulator protein	A, B, C, D, E, F, G, H, I	337	Caenorhabditis elegans	Mutation(s): 0  Gene Names: clhm-1, C44B7.4 Membrane Entity: Yes
UniProt
Find proteins for Q18593 (Caenorhabditis elegans) Explore Q18593  Go to UniProtKB:  Q18593

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Demura, K., Kusakizako, T., Shihoya, W., Hiraizumi, M., Shimada, H., Yamashita, K., Nishizawa, T., Nureki, O.

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2020-09-09
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2025-07-02
  Changes: Data collection