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Yorodumi- EMDB-28025: cryoEM structure of bovine bestrophin-2 and glutamine synthetase ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28025 | |||||||||
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Title | cryoEM structure of bovine bestrophin-2 and glutamine synthetase complex | |||||||||
Map data | local_filtered_map_locres | |||||||||
Sample |
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Keywords | ion channel / transport / anion channel / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Astrocytic Glutamate-Glutamine Uptake And Metabolism / Glutamate and glutamine metabolism / protein S-acyltransferase / intracellularly ligand-gated monoatomic ion channel activity / ligand-gated monoatomic anion channel activity / Stimuli-sensing channels / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / bicarbonate channel activity / regulation of sprouting angiogenesis ...Astrocytic Glutamate-Glutamine Uptake And Metabolism / Glutamate and glutamine metabolism / protein S-acyltransferase / intracellularly ligand-gated monoatomic ion channel activity / ligand-gated monoatomic anion channel activity / Stimuli-sensing channels / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / bicarbonate channel activity / regulation of sprouting angiogenesis / ligand-gated monoatomic cation channel activity / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / bicarbonate transport / chloride channel activity / chloride channel complex / basolateral plasma membrane / angiogenesis / endoplasmic reticulum / mitochondrion / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.0 Å | |||||||||
Authors | Owji AP / Kittredge AK / Yang T | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2022 Title: Bestrophin-2 and glutamine synthetase form a complex for glutamate release. Authors: Aaron P Owji / Kuai Yu / Alec Kittredge / Jiali Wang / Yu Zhang / Tingting Yang / Abstract: Bestrophin-2 (BEST2) is a member of the bestrophin family of calcium-activated anion channels that has a critical role in ocular physiology. Here we uncover a directional permeability of BEST2 to ...Bestrophin-2 (BEST2) is a member of the bestrophin family of calcium-activated anion channels that has a critical role in ocular physiology. Here we uncover a directional permeability of BEST2 to glutamate that heavily favours glutamate exit, identify glutamine synthetase (GS) as a binding partner of BEST2 in the ciliary body of the eye, and solve the structure of the BEST2-GS complex. BEST2 reduces cytosolic GS activity by tethering GS to the cell membrane. GS extends the ion conducting pathway of BEST2 through its central cavity and inhibits BEST2 channel function in the absence of intracellular glutamate, but sensitizes BEST2 to intracellular glutamate, which promotes the opening of BEST2 and thus relieves the inhibitory effect of GS. We demonstrate the physiological role of BEST2 in conducting chloride and glutamate and the influence of GS in non-pigmented ciliary epithelial cells. Together, our results reveal a novel mechanism of glutamate release through BEST2-GS. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28025.map.gz | 18.7 MB | EMDB map data format | |
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Header (meta data) | emd-28025-v30.xml emd-28025.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28025_fsc.xml | 21 KB | Display | FSC data file |
Images | emd_28025.png | 163.4 KB | ||
Masks | emd_28025_msk_1.map emd_28025_msk_2.map | 824 MB 824 MB | Mask map | |
Filedesc metadata | emd-28025.cif.gz | 6 KB | ||
Others | emd_28025_half_map_1.map.gz emd_28025_half_map_2.map.gz | 765.3 MB 765.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28025 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28025 | HTTPS FTP |
-Validation report
Summary document | emd_28025_validation.pdf.gz | 878.8 KB | Display | EMDB validaton report |
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Full document | emd_28025_full_validation.pdf.gz | 878.3 KB | Display | |
Data in XML | emd_28025_validation.xml.gz | 28 KB | Display | |
Data in CIF | emd_28025_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28025 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28025 | HTTPS FTP |
-Related structure data
Related structure data | 8ecyMC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28025.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | local_filtered_map_locres | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28025_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_28025_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: cryosparc half map1
File | emd_28025_half_map_1.map | ||||||||||||
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Annotation | cryosparc_half_map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryosparc half map2
File | emd_28025_half_map_2.map | ||||||||||||
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Annotation | cryosparc_half_map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Best2-GS
Entire | Name: Best2-GS |
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Components |
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-Supramolecule #1: Best2-GS
Supramolecule | Name: Best2-GS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-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: 47.424754 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 YWDAAEARAP YTAATAFLMQ QPSFQGSTFD ITLAKEDMQF QRQDGLEAPL NEAHGDFLQR LLPV GTGMG TGGLL UniProtKB: Bestrophin-2 |
-Macromolecule #2: Glutamine synthetase
Macromolecule | Name: Glutamine synthetase / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO / EC number: glutamine synthetase |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 42.085414 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MATSASSHLN KGIKQVYMAL PQGDKVQAMY IWIDGTGEGL RCKTRTLDSE PKCIEELPEW NFDGSSTFQS EGSNSDMYLV PAAMFRDPF RKDPNKLVFC EVFKYNRKPA ETNLRHTCKR IMDMVSNQRP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD ...String: MATSASSHLN KGIKQVYMAL PQGDKVQAMY IWIDGTGEGL RCKTRTLDSE PKCIEELPEW NFDGSSTFQS EGSNSDMYLV PAAMFRDPF RKDPNKLVFC EVFKYNRKPA ETNLRHTCKR IMDMVSNQRP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD KAYGRDIVEA HYRACLYAGI KIGGTNAEVM PAQWEFQIGP CEGIDMGDHL WVARFILHRV CEDFGVIATF DP KPIPGNW NGAGCHTNFS TKAMREENGL KYIEEAIEKL SKRHQYHIRA YDPKGGLDNA RRLTGFHETS NINDFSAGVA NRG ASIRIP RTVGQEKKGY FEDRRPSANC DPFAVTEALI RTCLLNETGD EPFQYKN UniProtKB: Glutamine synthetase |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #4: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 11 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #5: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 5 / Number of copies: 20 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 2024 / 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
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.16 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 |