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Yorodumi- EMDB-19066: TREK2 in OGNG/CHS detergent micelle with biparatopic inhibitory n... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19066 | |||||||||
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Title | TREK2 in OGNG/CHS detergent micelle with biparatopic inhibitory nanobody Nb6158 | |||||||||
Map data | TREK2 with linked inhibitory nanobody in OGNG CHS detergent micelle at pH 7.5 | |||||||||
Sample |
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Keywords | Ion channel / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium channel activity / potassium ion transmembrane transport / memory / signal transduction / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.37 Å | |||||||||
Authors | Smith KHM / Tucker SJ | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Extracellular modulation of TREK-2 activity with nanobodies provides insight into the mechanisms of K2P channel regulation. Authors: Karin E J Rödström / Alexander Cloake / Janina Sörmann / Agnese Baronina / Kathryn H M Smith / Ashley C W Pike / Jackie Ang / Peter Proks / Marcus Schewe / Ingelise Holland-Kaye / Simon R ...Authors: Karin E J Rödström / Alexander Cloake / Janina Sörmann / Agnese Baronina / Kathryn H M Smith / Ashley C W Pike / Jackie Ang / Peter Proks / Marcus Schewe / Ingelise Holland-Kaye / Simon R Bushell / Jenna Elliott / Els Pardon / Thomas Baukrowitz / Raymond J Owens / Simon Newstead / Jan Steyaert / Elisabeth P Carpenter / Stephen J Tucker / Abstract: Potassium channels of the Two-Pore Domain (K2P) subfamily, KCNK1-KCNK18, play crucial roles in controlling the electrical activity of many different cell types and represent attractive therapeutic ...Potassium channels of the Two-Pore Domain (K2P) subfamily, KCNK1-KCNK18, play crucial roles in controlling the electrical activity of many different cell types and represent attractive therapeutic targets. However, the identification of highly selective small molecule drugs against these channels has been challenging due to the high degree of structural and functional conservation that exists not only between K2P channels, but across the whole K channel superfamily. To address the issue of selectivity, here we generate camelid antibody fragments (nanobodies) against the TREK-2 (KCNK10) K2P K channel and identify selective binders including several that directly modulate channel activity. X-ray crystallography and CryoEM data of these nanobodies in complex with TREK-2 also reveal insights into their mechanisms of activation and inhibition via binding to the extracellular loops and Cap domain, as well as their suitability for immunodetection. These structures facilitate design of a biparatropic inhibitory nanobody with markedly improved sensitivity. Together, these results provide important insights into TREK channel gating and provide an alternative, more selective approach to modulation of K2P channel activity via their extracellular domains. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19066.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-19066-v30.xml emd-19066.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19066_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_19066.png | 33.1 KB | ||
Masks | emd_19066_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-19066.cif.gz | 5.4 KB | ||
Others | emd_19066_half_map_1.map.gz emd_19066_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19066 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19066 | HTTPS FTP |
-Validation report
Summary document | emd_19066_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_19066_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_19066_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_19066_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19066 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19066 | HTTPS FTP |
-Related structure data
Related structure data | 8qz1C 8qz2C 8qz3C 8qz4C 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_19066.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | TREK2 with linked inhibitory nanobody in OGNG CHS detergent micelle at pH 7.5 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19066_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19066_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19066_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of TREK2 and inhibitory nanobody Nb6158
Entire | Name: Complex of TREK2 and inhibitory nanobody Nb6158 |
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Components |
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-Supramolecule #1: Complex of TREK2 and inhibitory nanobody Nb6158
Supramolecule | Name: Complex of TREK2 and inhibitory nanobody Nb6158 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Macromolecule #1: TREK2
Macromolecule | Name: TREK2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MGLQTVMKWK TVVAIFVVVV VYLVTGGLVF RALEQPFESS QKNTIALEKA EFLRDHVCVS PQELETLIQH ALDADNAGVS PIGNSSNNSS HWDLGSAFFF AGTVITTIGY GNIAPSTEGG KIFCILYAIF GIPLFGFLLA GIGDQLGTIF GKSIARVEKV FRKKQVSQTK ...String: MGLQTVMKWK TVVAIFVVVV VYLVTGGLVF RALEQPFESS QKNTIALEKA EFLRDHVCVS PQELETLIQH ALDADNAGVS PIGNSSNNSS HWDLGSAFFF AGTVITTIGY GNIAPSTEGG KIFCILYAIF GIPLFGFLLA GIGDQLGTIF GKSIARVEKV FRKKQVSQTK IRVISTILFI LAGCIVFVTI PAVIFKYIEG WTALESIYFV VVTLTTVGFG DFVAGGNAGI NYREWYKPLV WFWILVGLAY FAAVLSMIGD WLRVLSKKTK EEVGEAENLY FQSHHHHHHH HHHDYKDDDD K UniProtKB: Potassium channel subfamily K member 10 |
-Macromolecule #2: Nb6158
Macromolecule | Name: Nb6158 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QVQLVESGGG LVQAGDSLRV SCAGSGFTFT SYGMGWFRQA PGKEREFVAS INWNSNTAYA DSVRGRFTIS RDNAESMMYL QMNSLKPEDT AVYYCAATRA YSKPRVDSRH YDYWGQGTQV TVSSGGGGSG GGGSGGGGSQ VQLVESGGGL VQAGGSLRLS CAASGRAGSG ...String: QVQLVESGGG LVQAGDSLRV SCAGSGFTFT SYGMGWFRQA PGKEREFVAS INWNSNTAYA DSVRGRFTIS RDNAESMMYL QMNSLKPEDT AVYYCAATRA YSKPRVDSRH YDYWGQGTQV TVSSGGGGSG GGGSGGGGSQ VQLVESGGGL VQAGGSLRLS CAASGRAGSG YAMGWFRQAP GKEREIVGAI SWSGDNTYYA DSVRGRVTIS RDYAQNTVYL QMNSLKPEDT AVYYCAADGR GNLRRGTAGR YVEYWGQGTQ VTVSSHHHHH HEPEA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.1 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |