+Open data
-Basic information
Entry | Database: PDB / ID: 7dsd | ||||||
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Title | CALHM1 close state with disordered CTH | ||||||
Components | Calcium homeostasis modulator 1 | ||||||
Keywords | MEMBRANE PROTEIN / close state | ||||||
Function / homology | Calcium homeostasis modulator family / Calcium homeostasis modulator / voltage-gated calcium channel activity / monoatomic cation channel activity / plasma membrane / Calcium homeostasis modulator 1 Function and homology information | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Ren, Y. / Yang, X. / Shen, Y.Q. | ||||||
Citation | Journal: J Biol Chem / Year: 2022 Title: Cryo-EM structure of the heptameric calcium homeostasis modulator 1 channel. Authors: Yue Ren / Yang Li / Yaojie Wang / Tianlei Wen / Xuhang Lu / Shenghai Chang / Xing Zhang / Yuequan Shen / Xue Yang / Abstract: Calcium homeostasis modulator 1 (CALHM1) is a voltage- and Ca-gated ATP channel that plays an important role in neuronal signaling. However, as the previously reported CALHM structures are all in the ...Calcium homeostasis modulator 1 (CALHM1) is a voltage- and Ca-gated ATP channel that plays an important role in neuronal signaling. However, as the previously reported CALHM structures are all in the ATP-conducting state, the gating mechanism of ATP permeation is still elusive. Here, we report cryo-EM reconstructions of two Danio rerio CALHM1 heptamers with ordered or flexible long C-terminal helices at resolutions of 3.2 Å and 2.9 Å, respectively, and one D. rerio CALHM1 octamer with flexible long C-terminal helices at a resolution of 3.5 Å. Structural analysis shows that the heptameric CALHM1s are in an ATP-nonconducting state with a central pore diameter of approximately 6.6 Å. Compared with those inside the octameric CALHM1, the N-helix inside the heptameric CALHM1 is in the "down" position to avoid steric clashing with the adjacent TM1 helix. Molecular dynamics simulations show that as the N-helix moves from the "down" position to the "up" position, the pore size of ATP molecule permeation increases significantly. Our results provide important information for elucidating the mechanism of ATP molecule permeation in the CALHM1 channel. | ||||||
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 | 7dsd.cif.gz | 243.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dsd.ent.gz | 195.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/7dsd ftp://data.pdbj.org/pub/pdb/validation_reports/ds/7dsd | HTTPS FTP |
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-Related structure data
Related structure data | 30831MC 7dscC 7dseC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 39801.129 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: calhm1 / Cell line (production host): HEK-293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: E7F2J4 #2: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CALHM1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Danio rerio (zebrafish) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK-293S GnTI- |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56801 / Symmetry type: POINT |