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- PDB-8gmq: Chicken CALHM1 purified from mammalian cells -

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Basic information

Entry
Database: PDB / ID: 8gmq
TitleChicken CALHM1 purified from mammalian cells
ComponentsCalcium homeostasis modulator 1
KeywordsMEMBRANE PROTEIN / taste / assembly / calcium homeostasis modulator protein / channel / lipid binding / large-pore channel
Function / homology
Function and homology information


sensory perception of bitter taste / sensory perception of umami taste / sensory perception of sweet taste / protein heterooligomerization / ATP export / regulation of monoatomic ion transmembrane transport / calcium-activated cation channel activity / plasma membrane raft / monoatomic cation channel activity / voltage-gated calcium channel activity ...sensory perception of bitter taste / sensory perception of umami taste / sensory perception of sweet taste / protein heterooligomerization / ATP export / regulation of monoatomic ion transmembrane transport / calcium-activated cation channel activity / plasma membrane raft / monoatomic cation channel activity / voltage-gated calcium channel activity / protein homooligomerization / basolateral plasma membrane / identical protein binding / plasma membrane
Similarity search - Function
Calcium homeostasis modulator family / Calcium homeostasis modulator
Similarity search - Domain/homology
Chem-POV / Calcium homeostasis modulator 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsSyrjanen, J.L. / Furukawa, H.
Funding support United States, 2items
OrganizationGrant numberCountry
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
CitationJournal: Nat Commun / Year: 2023
Title: Structure of human CALHM1 reveals key locations for channel regulation and blockade by ruthenium red.
Authors: Johanna L Syrjänen / Max Epstein / Ricardo Gómez / Hiro Furukawa /
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 ...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.
History
DepositionMar 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium homeostasis modulator 1
B: Calcium homeostasis modulator 1
C: Calcium homeostasis modulator 1
D: Calcium homeostasis modulator 1
E: Calcium homeostasis modulator 1
F: Calcium homeostasis modulator 1
G: Calcium homeostasis modulator 1
H: Calcium homeostasis modulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,60716
Polymers272,5268
Non-polymers6,0818
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Calcium homeostasis modulator 1


Mass: 34065.785 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CALHM1 / Cell line (production host): Hek293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: A0A8V0ZGE7
#2: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
Has ligand of interestY
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: Octameric chicken CALHM1 with lipids / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293 GnTI-
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 288.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1Warpparticle selection
2EPUimage acquisition
12RELION3D reconstruction
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188439 / Symmetry type: POINT

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