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Yorodumi- EMDB-19364: Structure of heteromeric CALHM2/4 channel in complex with synthet... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19364 | |||||||||
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Title | Structure of heteromeric CALHM2/4 channel in complex with synthetic nanobodies SbC2 and SbC4 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ion channel / large pore channels / sybody / CALHM / MEMBRANE PROTEIN | |||||||||
Function / homology | Calcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / positive regulation of apoptotic process / membrane / Calcium homeostasis modulator protein 4 / Calcium homeostasis modulator protein 2 Function and homology information | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.26 Å | |||||||||
Authors | Drozdzyk K / Dutzler R | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: To Be Published Title: Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs Authors: Drozdzyk K / Peter M / Dutzler R | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19364.map.gz | 79.2 MB | EMDB map data format | |
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Header (meta data) | emd-19364-v30.xml emd-19364.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19364_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_19364.png | 35.5 KB | ||
Filedesc metadata | emd-19364.cif.gz | 5.9 KB | ||
Others | emd_19364_half_map_1.map.gz emd_19364_half_map_2.map.gz | 77.8 MB 77.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19364 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19364 | HTTPS FTP |
-Validation report
Summary document | emd_19364_validation.pdf.gz | 918.9 KB | Display | EMDB validaton report |
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Full document | emd_19364_full_validation.pdf.gz | 918.5 KB | Display | |
Data in XML | emd_19364_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | emd_19364_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19364 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19364 | HTTPS FTP |
-Related structure data
Related structure data | 8rmmMC 8rmkC 8rmlC 8rmnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19364.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.302 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_19364_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19364_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of heteromeric CALHM2/4 channel with synthetic nanobody SbC4
Entire | Name: Complex of heteromeric CALHM2/4 channel with synthetic nanobody SbC4 |
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Components |
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-Supramolecule #1: Complex of heteromeric CALHM2/4 channel with synthetic nanobody SbC4
Supramolecule | Name: Complex of heteromeric CALHM2/4 channel with synthetic nanobody SbC4 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 0.541 kDa/nm |
-Macromolecule #1: Calcium homeostasis modulator protein 4
Macromolecule | Name: Calcium homeostasis modulator protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 35.981656 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Synthetic nanobody SbC4
Macromolecule | Name: Synthetic nanobody SbC4 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 12.87738 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
Sequence | String: QGPSQVQLVE SGGGLVQAGG SLRLSCAASG FPVYYTHMRW YRQAPGKERE WVAAIYSKGA GTHYADSVKG RFTISRDNAK NTVYLQMNS LKPEDTAVYY CFVGVGNSYI GQGTQVTVSA |
-Macromolecule #3: Calcium homeostasis modulator protein 2
Macromolecule | Name: Calcium homeostasis modulator protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.099535 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: Synthetic nanobody SbC2
Macromolecule | Name: Synthetic nanobody SbC2 / type: protein_or_peptide / ID: 4 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 14.067451 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
Sequence | String: QGPSQVQLVE SGGGSVQAGG SLRLSCAASG NIRNISYLGW FRQAPGKERE GVAALWTTQG QTYYADSVKG RFTVSLDNAK NTVYLQMNS LKPEDTALYY CAAATSGQYN PLRGYHYNEY WGQGTQVTVS A |
-Macromolecule #5: DIUNDECYL PHOSPHATIDYL CHOLINE
Macromolecule | Name: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 5 / Number of copies: 6 / Formula: PLC |
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Molecular weight | Theoretical: 622.834 Da |
Chemical component information | ChemComp-PLC: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |