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- PDB-8gmr: Cryo-EM structure of octameric human CALHM1 -

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Basic information

Entry
Database: PDB / ID: 8gmr
TitleCryo-EM structure of octameric human CALHM1
ComponentsCalcium homeostasis modulator protein 1
KeywordsMEMBRANE PROTEIN / taste / assembly / calcium homeostasis modulator protein / channel / lipid binding / large-pore channel
Function / homology
Function and homology information


Sensory perception of salty taste / ATP transport / sensory perception of bitter taste / sensory perception of umami taste / sensory perception of sweet taste / protein heterooligomerization / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / regulation of monoatomic ion transmembrane transport / response to stimulus ...Sensory perception of salty taste / ATP transport / sensory perception of bitter taste / sensory perception of umami taste / sensory perception of sweet taste / protein heterooligomerization / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / regulation of monoatomic ion transmembrane transport / response to stimulus / monoatomic cation transport / voltage-gated calcium channel activity / monoatomic cation channel activity / protein homooligomerization / Sensory perception of sweet, bitter, and umami (glutamate) taste / basolateral plasma membrane / endoplasmic reticulum 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 protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 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: Syrjanen, J.L. / Epstein, M. / Gomez, R. / Furukawa, H.
History
DepositionMar 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Structure summary / Category: em_entity_assembly / Item: _em_entity_assembly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)284,23616
Polymers278,1568
Non-polymers6,0818
Water0
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 protein 1 / Protein FAM26C


Mass: 34769.484 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALHM1, FAM26C / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q8IU99
#2: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC / POPC


Mass: 760.076 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
Has ligand of interestY

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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 human CALHM1 / 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: LEICA EM GP / Cryogen name: ETHANE

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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 FIELDBright-field microscopy / 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
9Cootmodel refinement
10PHENIXmodel refinement
13RELIONclassification
14RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35412 / Symmetry type: POINT

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