+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27136 | ||||||||||||
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Title | bBest2_345 Ca2+-bound open state | ||||||||||||
Map data | density modified (phenix.resolve) and resampled in coot (resample factor = 1.5) | ||||||||||||
Sample |
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Keywords | Ion channel / chloride channel / anion channel / pentamer / TRANSPORT PROTEIN | ||||||||||||
Function / homology | Function and homology information intracellularly ligand-gated monoatomic ion channel activity / ligand-gated monoatomic anion channel activity / Stimuli-sensing channels / bicarbonate channel activity / bicarbonate transport / chloride channel activity / ligand-gated monoatomic cation channel activity / chloride channel complex / basolateral plasma membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.93 Å | ||||||||||||
Authors | Owji AP / Kittredge A / Hendrickson WA / Tingting Y | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structures and gating mechanisms of human bestrophin anion channels. Authors: Aaron P Owji / Jiali Wang / Alec Kittredge / Zada Clark / Yu Zhang / Wayne A Hendrickson / Tingting Yang / Abstract: Bestrophin-1 (Best1) and bestrophin-2 (Best2) are two members of the bestrophin family of calcium (Ca)-activated chloride (Cl) channels with critical involvement in ocular physiology and direct ...Bestrophin-1 (Best1) and bestrophin-2 (Best2) are two members of the bestrophin family of calcium (Ca)-activated chloride (Cl) channels with critical involvement in ocular physiology and direct pathological relevance. Here, we report cryo-EM structures of wild-type human Best1 and Best2 in various states at up to 1.8 Å resolution. Ca-bound Best1 structures illustrate partially open conformations at the two Ca-dependent gates of the channels, in contrast to the fully open conformations observed in Ca-bound Best2, which is in accord with the significantly smaller currents conducted by Best1 in electrophysiological recordings. Comparison of the closed and open states reveals a C-terminal auto-inhibitory segment (AS), which constricts the channel concentrically by wrapping around the channel periphery in an inter-protomer manner and must be released to allow channel opening. Our results demonstrate that removing the AS from Best1 and Best2 results in truncation mutants with similar activities, while swapping the AS between Best1 and Best2 results in chimeric mutants with swapped activities, underlying a key role of the AS in determining paralog specificity among bestrophins. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27136.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-27136-v30.xml emd-27136.xml | 23 KB 23 KB | Display Display | EMDB header |
Images | emd_27136.png | 164.2 KB | ||
Filedesc metadata | emd-27136.cif.gz | 6.4 KB | ||
Others | emd_27136_additional_1.map.gz emd_27136_half_map_1.map.gz emd_27136_half_map_2.map.gz | 123.2 MB 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27136 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27136 | HTTPS FTP |
-Validation report
Summary document | emd_27136_validation.pdf.gz | 933 KB | Display | EMDB validaton report |
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Full document | emd_27136_full_validation.pdf.gz | 932.5 KB | Display | |
Data in XML | emd_27136_validation.xml.gz | 15 KB | Display | |
Data in CIF | emd_27136_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27136 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27136 | HTTPS FTP |
-Related structure data
Related structure data | 8d1nMC 8d1eC 8d1fC 8d1gC 8d1hC 8d1iC 8d1jC 8d1kC 8d1lC 8d1mC 8d1oC C: citing same article (ref.) M: atomic model generated by this map |
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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_27136.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | density modified (phenix.resolve) and resampled in coot (resample factor = 1.5) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.5478 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: full map
File | emd_27136_additional_1.map | ||||||||||||
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Annotation | full map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_27136_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_27136_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : bBest2_345 Ca2+-bound open state
Entire | Name: bBest2_345 Ca2+-bound open state |
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Components |
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-Supramolecule #1: bBest2_345 Ca2+-bound open state
Supramolecule | Name: bBest2_345 Ca2+-bound open state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 210 KDa |
-Macromolecule #1: Bestrophin
Macromolecule | Name: Bestrophin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 40.408918 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MTVTYTARVA KARFGGFSKL LLLWRGSIYK LLWRELLCFL GLFMALSAAY RFVLTEEQKR YFEKLVLYCD RYASLIPVSF VLGFYVTLV VHRWWNQYLS MPLTDALMCV VVGTVHGHDE RGRLYRRTLM RYAGLSGVLI LRSVSTAVFK RFPTIDHVVE A GFMTREER ...String: MTVTYTARVA KARFGGFSKL LLLWRGSIYK LLWRELLCFL GLFMALSAAY RFVLTEEQKR YFEKLVLYCD RYASLIPVSF VLGFYVTLV VHRWWNQYLS MPLTDALMCV VVGTVHGHDE RGRLYRRTLM RYAGLSGVLI LRSVSTAVFK RFPTIDHVVE A GFMTREER KKFENLNSSY NKYWVPCVWF CNLAAQARRE GRIRDNGAFK LLLEELNVFR SKCGMLFHYD WISVPLVYTQ VV TIAVYSY FLACLIGRQF LDPAQGYKDH DLDLCVPIFT LLQFFFYAGW LKVAEQLINP FGEDDDDFET NFLIDRCFQV SML AVDEMY DDLAMLEKDL YWDAAEARA UniProtKB: Bestrophin-2 |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #3: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 50 / Formula: MC3 |
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Molecular weight | Theoretical: 677.933 Da |
Chemical component information | ChemComp-MC3: |
-Macromolecule #4: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13...
Macromolecule | Name: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol type: ligand / ID: 4 / Number of copies: 5 / Formula: DU0 |
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Molecular weight | Theoretical: 516.752 Da |
Chemical component information | ChemComp-DU0: |
-Macromolecule #5: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 600 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | ||||||||||||
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Buffer | pH: 7.8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | bBest2_345 Ca2+-bound open state |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 3203 / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |