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- EMDB-30016: Cryo-EM structure of the calcium homeostasis modulator 1 channel -

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Basic information

Entry
Database: EMDB / ID: EMD-30016
TitleCryo-EM structure of the calcium homeostasis modulator 1 channel
Map data
Sample
  • Cell: CALHM1 channel
    • Protein or peptide: Calcium homeostasis modulator 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsOctamer / MEMBRANE PROTEIN
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator / ATP export / voltage-gated calcium channel activity / plasma membrane / Calcium homeostasis modulator 1
Function and homology information
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRen Y / Yang X
Funding support China, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504801 China
National Natural Science Foundation of China (NSFC)91954119 China
National Natural Science Foundation of China (NSFC)31870736 China
National Natural Science Foundation of China (NSFC)31570750 China
National Natural Science Foundation of China (NSFC)31870834 China
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM structure of the calcium homeostasis modulator 1 channel.
Authors: Yue Ren / Tianlei Wen / Zhiqin Xi / Shunjin Li / Jing Lu / Xing Zhang / Xue Yang / Yuequan Shen /
Abstract: Calcium homeostasis modulator 1 (CALHM1) is a voltage-gated ATP release channel that plays an important role in neural gustatory signaling and the pathogenesis of Alzheimer's disease. Here, we ...Calcium homeostasis modulator 1 (CALHM1) is a voltage-gated ATP release channel that plays an important role in neural gustatory signaling and the pathogenesis of Alzheimer's disease. Here, we present a cryo-electron microscopy structure of full-length Ca-free CALHM1 from Danio rerio at an overall resolution of 3.1 Å. Our structure reveals an octameric architecture with a wide pore diameter of ~20 Å, presumably representing the active conformation. The overall structure is substantially different from that of the isoform CALHM2, which forms both undecameric hemichannels and gap junctions. The N-terminal small helix folds back to the pore and forms an antiparallel interaction with transmembrane helix 1. Structural analysis revealed that the extracellular loop 1 region within the dimer interface may contribute to oligomeric assembly. A positive potential belt inside the pore was identified that may modulate ion permeation. Our structure offers insights into the assembly and gating mechanism of the CALHM1 channel.
History
DepositionFeb 14, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lyg
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30016.png

Downloads & links

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Map

FileDownload / File: emd_30016.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 260 pix.
= 263.64 Å		1.01 Å/pix.
x 260 pix.
= 263.64 Å		1.01 Å/pix.
x 260 pix.
= 263.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.053630132 - 0.109043986
Average (Standard dev.)0.00019120394 (±0.0027916662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 263.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z263.640263.640263.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0540.1090.000

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Supplemental data

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Sample components

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Entire : CALHM1 channel

EntireName: CALHM1 channel
Components
  • Cell: CALHM1 channel
    • Protein or peptide: Calcium homeostasis modulator 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: CALHM1 channel

SupramoleculeName: CALHM1 channel / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)

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Macromolecule #1: Calcium homeostasis modulator 1

MacromoleculeName: Calcium homeostasis modulator 1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 41.213645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LEQKLISEED LRSDKFRIMV QFLQANQESF MNGICGIMAL ASAQMYSSFE FTCPCLPDYN YAYGIGILIV PPIWFFLLGY VMNNNISVL TEEWKRPVGK RSKDPAVLRY MFSSMTQRAL IAPAVWIAVT LMDGKSFLCA FSPTADLSEF VNESYQSLSQ K ELLKIQAK ...String:
LEQKLISEED LRSDKFRIMV QFLQANQESF MNGICGIMAL ASAQMYSSFE FTCPCLPDYN YAYGIGILIV PPIWFFLLGY VMNNNISVL TEEWKRPVGK RSKDPAVLRY MFSSMTQRAL IAPAVWIAVT LMDGKSFLCA FSPTADLSEF VNESYQSLSQ K ELLKIQAK IPCKDIFEEH EIISREAATR YIRCLSQACG WTFLMVITLV AFLVRAIRPC FTQAAFLKTK YWSHYIDTER KL FDETCKE HAKSFAKVCI QQYFESISGE IVSQLPQSPA KKGKGNKDED GEKQKSDEER LLGIRKEGDM NKVLWNWHTC KPP LLLSKR TEEMNGHAHL DTHSLTDERH TKKKAVVYYS KV

UniProtKB: Calcium homeostasis modulator 1

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initial by Cryosparc2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59833
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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