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- PDB-6lmt: Cryo-EM structure of the killifish CALHM1 -

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Entry
Database: PDB / ID: 6lmt
TitleCryo-EM structure of the killifish CALHM1
ComponentsCalcium homeostasis modulator 1
KeywordsMEMBRANE PROTEIN / channel
Function / homology
Function and homology information


ATP export / monoatomic cation channel activity / calcium channel activity / basolateral plasma membrane / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
Calcium homeostasis modulator family / Calcium homeostasis modulator
Similarity search - Domain/homology
CHOLESTEROL HEMISUCCINATE / Calcium homeostasis modulator 1
Similarity search - Component
Biological speciesOryzias latipes (Japanese medaka)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsDemura, K. / Kusakizako, T. / Shihoya, W. / Hiraizumi, M. / Shimada, H. / Yamashita, K. / Nishizawa, T. / Nureki, O.
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM structures of calcium homeostasis modulator channels in diverse oligomeric assemblies.
Authors: Kanae Demura / Tsukasa Kusakizako / Wataru Shihoya / Masahiro Hiraizumi / Kengo Nomura / Hiroto Shimada / Keitaro Yamashita / Tomohiro Nishizawa / Akiyuki Taruno / Osamu Nureki /
Abstract: Calcium homeostasis modulator (CALHM) family proteins are Ca-regulated adenosine triphosphate (ATP)-release channels involved in neural functions including neurotransmission in gustation. Here, we ...Calcium homeostasis modulator (CALHM) family proteins are Ca-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 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.
History
DepositionDec 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
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Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
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Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
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Structure visualization

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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)295,89340
Polymers280,3178
Non-polymers15,57532
Water00
1


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

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Components

#1: Protein
Calcium homeostasis modulator 1


Mass: 35039.684 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryzias latipes (Japanese medaka) / Gene: CALHM1 / Production host: Homo sapiens (human) / References: UniProt: H2MCM1
#2: Chemical...
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
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: CALHM1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Oryzias latipes (Japanese medaka)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 59 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102109 / Symmetry type: POINT

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