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- EMDB-19362: Cryo-EM structure of human CALHM2 in complex with synthetic nanob... -

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Basic information

Entry
Database: EMDB / ID: EMD-19362
TitleCryo-EM structure of human CALHM2 in complex with synthetic nanobody SbC2
Map data
Sample
  • Complex: Complex of CALHM2 channel with synthetic nanobody SbC2
    • Protein or peptide: Calcium homeostasis modulator protein 2
    • Protein or peptide: Synthetic nanobody SbC2
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
Keywordsion channel / large pore channels / sybody / CALHM / MEMBRANE PROTEIN
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / positive regulation of apoptotic process / membrane / Calcium homeostasis modulator protein 2
Function and homology information
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsDrozdzyk K / Dutzler R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs
Authors: Drozdzyk K / Peter M / Dutzler R
History
DepositionJan 8, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19362.png

Downloads & links

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Map

FileDownload / File: emd_19362.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.282
Minimum - Maximum-1.1984948 - 2.180273
Average (Standard dev.)0.0075840624 (±0.05733633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19362_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19362_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of CALHM2 channel with synthetic nanobody SbC2

EntireName: Complex of CALHM2 channel with synthetic nanobody SbC2
Components
  • Complex: Complex of CALHM2 channel with synthetic nanobody SbC2
    • Protein or peptide: Calcium homeostasis modulator protein 2
    • Protein or peptide: Synthetic nanobody SbC2
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE

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Supramolecule #1: Complex of CALHM2 channel with synthetic nanobody SbC2

SupramoleculeName: Complex of CALHM2 channel with synthetic nanobody SbC2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 590 KDa

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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: 37.099535 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAALIAENF RFLSLFFKSK DVMIFNGLVA LGTVGSQELF SVVAFHCPCS PARNYLYGLA AIGVPALVLF IIGIILNNHT WNLVAECQH RRTKNCSAAP TFLLLSSILG RAAVAPVTWS VISLLRGEAY VCALSEFVDP SSLTAREEHF PSAHATEILA R FPCKENPD ...String:
MSAALIAENF RFLSLFFKSK DVMIFNGLVA LGTVGSQELF SVVAFHCPCS PARNYLYGLA AIGVPALVLF IIGIILNNHT WNLVAECQH RRTKNCSAAP TFLLLSSILG RAAVAPVTWS VISLLRGEAY VCALSEFVDP SSLTAREEHF PSAHATEILA R FPCKENPD NLSDFREEVS RRLRYESQLF GWLLIGVVAI LVFLTKCLKH YCSPLSYRQE AYWAQYRANE DQLFQRTAEV HS RVLAANN VRRFFGFVAL NKDDEELIAN FPVEGTQPRP QWNAITGVYL YRENQGLPLY SRLHKWAQGL AGNGAAPDNV EMA LLPSAL EVLFQ

UniProtKB: Calcium homeostasis modulator protein 2

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Macromolecule #2: Synthetic nanobody SbC2

MacromoleculeName: Synthetic nanobody SbC2 / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 16.80334 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
SSSQVQLVES GGGSVQAGGS LRLSCAASGN IRNISYLGWF RQAPGKEREG VAALWTTQGQ TYYADSVKGR FTVSLDNAKN TVYLQMNSL KPEDTALYYC AAATSGQYNP LRGYHYNEYW GQGTQVTVSA GRAGEQKLIS EEDLNSAVDH HHHHH

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Macromolecule #3: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 3 / Number of copies: 11 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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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: 7.6
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 72.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C11 (11 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37894
FSC plot (resolution estimation)

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