8GMP

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)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

(2023) Nat Commun 14: 3821-3821

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.

Organizational Affiliation

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

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium homeostasis modulator protein 1	A [auth C] B [auth A] C [auth B] D E A [auth C], B [auth A], C [auth B], 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IU99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth G] SDF format, chain P [auth H] MOL2 format, chain I [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth G] MOL2 format, chain P [auth H]	I [auth C] J [auth A] K [auth B] L [auth D] M [auth E] I [auth C], J [auth A], K [auth B], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain I [auth C] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth C] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Entry History & Funding Information

Deposition Author(s):

Syrjanen, J.L.

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	--