+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7824 | |||||||||
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Title | Cryo-EM structure of human TRPV6-Y467A in amphipols | |||||||||
Map data | primary map | |||||||||
Sample |
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Keywords | Ion channels / transporter / calcium channel / epithelial calcium channel / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information parathyroid hormone secretion / regulation of calcium ion-dependent exocytosis / TRP channels / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / calcium ion transmembrane transport / response to calcium ion / calcium channel activity / calcium ion transport ...parathyroid hormone secretion / regulation of calcium ion-dependent exocytosis / TRP channels / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / calcium ion transmembrane transport / response to calcium ion / calcium channel activity / calcium ion transport / calmodulin binding / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.34 Å | |||||||||
Authors | Singh AK / Saotome K | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural bases of TRP channel TRPV6 allosteric modulation by 2-APB. Authors: Appu K Singh / Kei Saotome / Luke L McGoldrick / Alexander I Sobolevsky / Abstract: Transient receptor potential (TRP) channels are involved in various physiological processes, including sensory transduction. The TRP channel TRPV6 mediates calcium uptake in epithelia and its ...Transient receptor potential (TRP) channels are involved in various physiological processes, including sensory transduction. The TRP channel TRPV6 mediates calcium uptake in epithelia and its expression is dramatically increased in numerous types of cancer. TRPV6 inhibitors suppress tumor growth, but the molecular mechanism of inhibition remains unknown. Here, we present crystal and cryo-EM structures of human and rat TRPV6 bound to 2-aminoethoxydiphenyl borate (2-APB), a TRPV6 inhibitor and modulator of numerous TRP channels. 2-APB binds to TRPV6 in a pocket formed by the cytoplasmic half of the S1-S4 transmembrane helix bundle. Comparing human wild-type and high-affinity mutant Y467A structures, we show that 2-APB induces TRPV6 channel closure by modulating protein-lipid interactions. Mutagenesis and functional analyses suggest that the identified 2-APB binding site might be present in other members of vanilloid subfamily TRP channels. Our findings reveal a mechanism of ion channel allosteric modulation that can be exploited for therapeutic design. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7824.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-7824-v30.xml emd-7824.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_7824.png | 238.6 KB | ||
Filedesc metadata | emd-7824.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7824 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7824 | HTTPS FTP |
-Validation report
Summary document | emd_7824_validation.pdf.gz | 430.5 KB | Display | EMDB validaton report |
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Full document | emd_7824_full_validation.pdf.gz | 430.1 KB | Display | |
Data in XML | emd_7824_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_7824_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7824 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7824 | HTTPS FTP |
-Related structure data
Related structure data | 6d7sMC 7825C 6d7oC 6d7pC 6d7qC 6d7tC 6d7vC 6d7xC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7824.map.gz / Format: CCP4 / Size: 32.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TRPV6 in amphipols
Entire | Name: TRPV6 in amphipols |
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Components |
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-Supramolecule #1: TRPV6 in amphipols
Supramolecule | Name: TRPV6 in amphipols / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Transient receptor potential cation channel subfamily V member 6
Macromolecule | Name: Transient receptor potential cation channel subfamily V member 6 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 85.076859 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGLSLPKEKG LILCLWSKFC RWFQRRESWA QSRDEQNLLQ QKRIWESPLL LAAKDNDVQA LNKLLKYEDC KVHQRGAMGE TALHIAALY DNLEAAMVLM EAAPELVFEP MTSELYEGQT ALHIAVVNQN MNLVRALLAR RASVSARATG TAFRRSPCNL I YFGEHPLS ...String: MGLSLPKEKG LILCLWSKFC RWFQRRESWA QSRDEQNLLQ QKRIWESPLL LAAKDNDVQA LNKLLKYEDC KVHQRGAMGE TALHIAALY DNLEAAMVLM EAAPELVFEP MTSELYEGQT ALHIAVVNQN MNLVRALLAR RASVSARATG TAFRRSPCNL I YFGEHPLS FAACVNSEEI VRLLIEHGAD IRAQDSLGNT VLHILILQPN KTFACQMYNL LLSYDRHGDH LQPLDLVPNH QG LTPFKLA GVEGNTVMFQ HLMQKRKHTQ WTYGPLTSTL YDLTEIDSSG DEQSLLELII TTKKREARQI LDQTPVKELV SLK WKRYGR PYFCMLGAIY LLYIICFTMC CIYRPLKPRT NNRTSPRDNT LLQQKLLQEA YMTPKDDIRL VGELVTVIGA IIIL LVEVP DIFRMGVTRF FGQTILGGPF HVLIITYAFM VLVTMVMRLI SASGEVVPMS FALVLGWCNV MAFARGFQML GPFTI MIQK MIFGDLMRFC WLMAVVILGF ASAFYIIFQT EDPEELGHFY DYPMALFSTF ELFLTIIDGP ANYNVDLPFM YSITYA AFA IIATLLMLNL LIAMMGDTHW RVAHERDELW RAQIVATTVM LERKLPRCLW PRSGICGREY GLGDRWFLRV EDRQDLN RQ RIQRYAQAFH TRGSEDLDKD SVEKLELGCP FSPHLSLPMP SVSRSTSRSS ANWERLRQGT LRRDLRGIIN RGLEDGES W EYQILVPRGS AAAWSHPQFE K UniProtKB: Transient receptor potential cation channel subfamily V member 6 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 115126 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |