8S90

Cryo-EM structure of octameric human CALHM1 (I109W) in complex with ruthenium red (C1)

• PDB DOI: https://doi.org/10.2210/pdb8S90/pdb
• EM Map EMD-40233: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2023-03-27 Released: 2023-07-26 
• Deposition Author(s): Syrjanen, J.L., Furukawa, H.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of human CALHM1 reveals key locations for channel regulation and blockade by ruthenium red.

Syrjanen, J.L., Epstein, M., Gomez, R., Furukawa, H.

(2023) Nat Commun 14: 3821-3821

• PubMed: 37380652 
• DOI: https://doi.org/10.1038/s41467-023-39388-3
• Primary Citation of Related Structures:  
  8GMP, 8GMQ, 8GMR, 8S8Z, 8S90


• PubMed Abstract: 
  

  Calcium homeostasis modulator 1 (CALHM1) is a voltage-dependent channel involved in neuromodulation and gustatory signaling. Despite recent progress in the structural biology of CALHM1, insights into functional regulation, pore architecture, and channel blockade remain limited. Here we present the cryo-EM structure of human CALHM1, revealing an octameric assembly pattern similar to the non-mammalian CALHM1s and the lipid-binding pocket conserved across species. We demonstrate by MD simulations that this pocket preferentially binds a phospholipid over cholesterol to stabilize its structure and regulate the channel activities. Finally, we show that residues in the amino-terminal helix form the channel pore that ruthenium red binds and blocks.

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Organizational Affiliation: 

W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C8  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 279.3 kDa 
• Atom Count: 15,323 
• Modelled Residue Count: 2,096 
• Deposited Residue Count: 2,512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium homeostasis modulator protein 1	A [auth B], B [auth A], C, D, E, F, G, H	314	Homo sapiens	Mutation(s): 1  Gene Names: CALHM1, FAM26C Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IU99 (Homo sapiens) Explore Q8IU99  Go to UniProtKB:  Q8IU99
PHAROS:  Q8IU99 GTEx:  ENSG00000185933

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R2R (Subject of Investigation/LOI)	I [auth E]	ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2) H28 N14 O2 Ru3 FOOPNNMQSUSGAT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Syrjanen, J.L., Furukawa, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	--
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	--

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references