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- EMDB-19365: Cryo-EM structure of a dimer of decameric human CALHM4 in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-19365
TitleCryo-EM structure of a dimer of decameric human CALHM4 in complex with synthetic nanobody SbC4
Map data
Sample
  • Complex: Complex of CALHM4 channel with synthetic nanobody SbC4
    • Protein or peptide: Calcium homeostasis modulator protein 4
    • Protein or peptide: Synthetic nanobody SbC4
Keywordsion channel / large pore channels / sybody / CALHM / MEMBRANE PROTEIN
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / membrane / Calcium homeostasis modulator protein 4
Function and homology information
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsPeter M / Drozdzyk 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_19365.png

Downloads & links

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Map

FileDownload / File: emd_19365.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 500 pix.
= 325.5 Å		0.65 Å/pix.
x 500 pix.
= 325.5 Å		0.65 Å/pix.
x 500 pix.
= 325.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0058
Minimum - Maximum-0.013682856 - 0.027927626
Average (Standard dev.)-0.000014494297 (±0.0012333434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 325.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19365_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_19365_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 CALHM4 channel with synthetic nanobody SbC4

EntireName: Complex of CALHM4 channel with synthetic nanobody SbC4
Components
  • Complex: Complex of CALHM4 channel with synthetic nanobody SbC4
    • Protein or peptide: Calcium homeostasis modulator protein 4
    • Protein or peptide: Synthetic nanobody SbC4

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Supramolecule #1: Complex of CALHM4 channel with synthetic nanobody SbC4

SupramoleculeName: Complex of CALHM4 channel with synthetic nanobody SbC4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.03 MDa

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Macromolecule #1: Calcium homeostasis modulator protein 4

MacromoleculeName: Calcium homeostasis modulator protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.981656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSCPTLNNIV SSLQRNGIFI NSLIAALTIG GQQLFSSSTF SCPCQVGKNF YYGSAFLVIP ALILLVAGFA LRSQMWTITG EYCCSCAPP YRRISPLECK LACLRFFSIT GRAVIAPLTW LAVTLLTGTY YECAASEFAS VDHYPMFDNV SASKREEILA G FPCCRSAP ...String:
MSCPTLNNIV SSLQRNGIFI NSLIAALTIG GQQLFSSSTF SCPCQVGKNF YYGSAFLVIP ALILLVAGFA LRSQMWTITG EYCCSCAPP YRRISPLECK LACLRFFSIT GRAVIAPLTW LAVTLLTGTY YECAASEFAS VDHYPMFDNV SASKREEILA G FPCCRSAP SDVILVRDEI ALLHRYQSQM LGWILITLAT IAALVSCCVA KCCSPLTSLQ HCYWTSHLQN ERELFEQAAE QH SRLLMMH RIKKLFGFIP GSEDVKHIRI PSCQDWKDIS VPTLLCMGDD LQGHYSFLGN RVDEDNEEDR SRGIELKPAL EVL FQ

UniProtKB: Calcium homeostasis modulator protein 4

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Macromolecule #2: Synthetic nanobody SbC4

MacromoleculeName: Synthetic nanobody SbC4 / type: protein_or_peptide / ID: 2 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.613268 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SSSQVQLVES GGGLVQAGGS LRLSCAASGF PVYYTHMRWY RQAPGKEREW VAAIYSKGAG THYADSVKGR FTISRDNAKN TVYLQMNSL KPEDTAVYYC FVGVGNSYIG QGTQVTVSAG RAGEQKLISE EDLNSAVDHH HHHH

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 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: D10 (2x10 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52248
FSC plot (resolution estimation)

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