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- EMDB-20789: Cryo-EM structure of human CALHM2 in a ruthenium red-bound inhibi... -

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Basic information

Entry
Database: EMDB / ID: EMD-20789
TitleCryo-EM structure of human CALHM2 in a ruthenium red-bound inhibited state
Map data
Samplehuman CALHM2:
Calcium homeostasis modulator protein 2 / ligand
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator protein 2 / cation channel activity / positive regulation of apoptotic process / integral component of plasma membrane / Calcium homeostasis modulator protein 2
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLu W / Du J / Choi W
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.
Validation ReportPDB-ID: 6uiw

SummaryFull reportAbout validation report
History
DepositionOct 1, 2019-
Header (metadata) releaseOct 9, 2019-
Map releaseNov 27, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uiw
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20789.png

Downloads & links

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Map

FileDownload / File: emd_20789.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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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: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.024086695 - 0.08078838
Average (Standard dev.)0.00002727001 (±0.0021338053)
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/NZ111-94150
NX/NY/NZ111123111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0240.0810.000

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Supplemental data

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Segmentation: #1

Fileemd_20789_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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

Fileemd_20789_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 lifted S1. This...

Fileemd_20789_additional_2.map
AnnotationMap of single subunit with lifted 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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Additional map: Map of single subunit with vertical S1. This...

Fileemd_20789_additional_3.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 / Number of components: 3

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Component #1: protein, human CALHM2

ProteinName: human CALHM2 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Calcium homeostasis modulator protein 2

ProteinName: Calcium homeostasis modulator protein 2 / Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 37.198676 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)

LigandName: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)
Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 0.559525 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 54.4 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C11 (11 fold cyclic) / Number of projections: 83728
3D reconstructionSoftware: RELION / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

6uiw

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