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- EMDB-20788: Cryo-EM structure of human CALHM2 in an active/open state -

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Basic information

Entry
Database: EMDB / ID: EMD-20788
TitleCryo-EM structure of human CALHM2 in an active/open state
Map dataFinal map refined with a soft solvent mask. Improved resolution for the well-defined parts of the protein, yet incomplete densities for the highly flexible regions such as S1.
Sample
  • Complex: human CALHM2
    • Protein or peptide: Calcium homeostasis modulator protein 2
Keywordscalcium homeostasis modulator / CALHM2 / TRANSPORT PROTEIN
Function / homology
Function and homology information


regulation of microglial cell activation / ATP export / calcium ion import / monoatomic cation channel activity / regulation of synaptic plasticity / positive regulation of apoptotic process / plasma membrane
Similarity search - Function
Calcium homeostasis modulator family / Calcium homeostasis modulator
Similarity search - Domain/homology
Calcium homeostasis modulator protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLu W / Du J
CitationJournal: Nature / Year: 2019
Title: The structures and gating mechanism of human calcium homeostasis modulator 2.
Authors: Wooyoung Choi / Nicolina Clemente / Weinan Sun / Juan Du / Wei Lü /
Abstract: Calcium homeostasis modulators (CALHMs) are voltage-gated, Ca-inhibited nonselective ion channels that act as major ATP release channels, and have important roles in gustatory signalling and neuronal ...Calcium homeostasis modulators (CALHMs) are voltage-gated, Ca-inhibited nonselective ion channels that act as major ATP release channels, and have important roles in gustatory signalling and neuronal toxicity. Dysfunction of CALHMs has previously been linked to neurological disorders. Here we present cryo-electron microscopy structures of the human CALHM2 channel in the Ca-free active or open state and in the ruthenium red (RUR)-bound inhibited state, at resolutions up to 2.7 Å. Our work shows that purified CALHM2 channels form both gap junctions and undecameric hemichannels. The protomer shows a mirrored arrangement of the transmembrane domains (helices S1-S4) relative to other channels with a similar topology, such as connexins, innexins and volume-regulated anion channels. Upon binding to RUR, we observed a contracted pore with notable conformational changes of the pore-lining helix S1, which swings nearly 60° towards the pore axis from a vertical to a lifted position. We propose a two-section gating mechanism in which the S1 helix coarsely adjusts, and the N-terminal helix fine-tunes, the pore size. We identified a RUR-binding site near helix S1 that may stabilize this helix in the lifted conformation, giving rise to channel inhibition. Our work elaborates on the principles of CALHM2 channel architecture and symmetry, and the mechanism that underlies channel inhibition.
History
DepositionOct 1, 2019-
Header (metadata) releaseOct 9, 2019-
Map releaseNov 27, 2019-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0105
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0105
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uiv
  • Surface level: 0.0105
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20788.png

Downloads & links

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Map

FileDownload / File: emd_20788.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map refined with a soft solvent mask. Improved resolution for the well-defined parts of the protein, yet incomplete densities for the highly flexible regions such as S1.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 340 pix.
= 348.84 Å		1.03 Å/pix.
x 340 pix.
= 348.84 Å		1.03 Å/pix.
x 340 pix.
= 348.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.026 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0105 / Movie #1: 0.0105
Minimum - Maximum-0.017790755 - 0.054619186
Average (Standard dev.)0.000024237006 (±0.0016764055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 348.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0261.0261.026
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z348.840348.840348.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0180.0550.000

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Supplemental data

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Mask #1

Fileemd_20788_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map refined without a soft solvent mask. Better...

Fileemd_20788_additional_1.map
AnnotationMap refined without a soft solvent mask. Better visualization of the highly flexible regions such as S1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map of single subunit with vertical S1. This...

Fileemd_20788_additional_2.map
AnnotationMap of single subunit with vertical S1. This map is obtained through symmetry expansion and signal subtraction of single subunit, followed by 3D classification.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human CALHM2

EntireName: human CALHM2
Components
  • Complex: human CALHM2
    • Protein or peptide: Calcium homeostasis modulator protein 2

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Supramolecule #1: human CALHM2

SupramoleculeName: human CALHM2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Calcium homeostasis modulator protein 2

MacromoleculeName: Calcium homeostasis modulator protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.198676 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAALIAENFR FLSLFFKSKD VMIFNGLVAL GTVGSQELFS VVAFHCPCSP ARNYLYGLAA IGVPALVLFI IGIILNNHTW NLVAECQHR RTKNCSAAPT FLLLSSILGR AAVAPVTWSV ISLLRGEAYV CALSEFVDPS SLTAREEHFP SAHATEILAR F PCKENPDN ...String:
MAALIAENFR FLSLFFKSKD VMIFNGLVAL GTVGSQELFS VVAFHCPCSP ARNYLYGLAA IGVPALVLFI IGIILNNHTW NLVAECQHR RTKNCSAAPT FLLLSSILGR AAVAPVTWSV ISLLRGEAYV CALSEFVDPS SLTAREEHFP SAHATEILAR F PCKENPDN LSDFREEVSR RLRYESQLFG WLLIGVVAIL VFLTKCLKHY CSPLSYRQEA YWAQYRANED QLFQRTAEVH SR VLAANNV RRFFGFVALN KDDEELIANF PVEGTQPRPQ WNAITGVYLY RENQGLPLYS RLHKWAQGLA GNGAAPDNVE MAL LPSFES RLVPR

UniProtKB: Calcium homeostasis modulator protein 2

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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

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 576174
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C11 (11 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 84858
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 300)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6uiv:
Cryo-EM structure of human CALHM2 in an active/open state

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