+Open data
-Basic information
Entry | Database: PDB / ID: 6lmt | ||||||
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Title | Cryo-EM structure of the killifish CALHM1 | ||||||
Components | Calcium homeostasis modulator 1 | ||||||
Keywords | MEMBRANE 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 | ||||||
Biological species | Oryzias latipes (Japanese medaka) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å | ||||||
Authors | Demura, K. / Kusakizako, T. / Shihoya, W. / Hiraizumi, M. / Shimada, H. / Yamashita, K. / Nishizawa, T. / Nureki, O. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6lmt.cif.gz | 374.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lmt.ent.gz | 326.3 KB | Display | PDB format |
PDBx/mmJSON format | 6lmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lmt_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 6lmt_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 6lmt_validation.xml.gz | 76.3 KB | Display | |
Data in CIF | 6lmt_validation.cif.gz | 97.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/6lmt ftp://data.pdbj.org/pub/pdb/validation_reports/lm/6lmt | HTTPS FTP |
-Related structure data
Related structure data | 0919MC 0920C 0921C 0922C 0923C 6lmuC 6lmvC 6lmwC 6lmxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10444 (Title: Cryo-EM structures of calcium homeostasis modulator (CALHM) channels Data size: 6.8 TB Data #1: Unaligned movies for OlCALHM1 [micrographs - multiframe] Data #2: Unaligned movies for HsCALHM2 [micrographs - multiframe] Data #3: Unaligned movies for CeCLHM-1 [micrographs - multiframe] Data #4: Unaligned movies for OlCALHM1-HsCALHM2 chimera [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CALHM1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Oryzias latipes (Japanese medaka) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 59 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102109 / Symmetry type: POINT |