+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41238 | |||||||||
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Title | VMAT1 dimer in unbound form and with reserpine | |||||||||
Map data | VMAT1 dimer in unbound form and with reserpine | |||||||||
Sample |
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Keywords | VMAT / SLC18 / vascular monoamine transporter / monoamines / neurotransmitters / reserpine / MEMBRANE PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Ye J / Liu B / Li W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2024 Title: Structural insights into vesicular monoamine storage and drug interactions. Authors: Jin Ye / Huaping Chen / Kaituo Wang / Yi Wang / Aaron Ammerman / Samjhana Awasthi / Jinbin Xu / Bin Liu / Weikai Li / Abstract: Biogenic monoamines-vital transmitters orchestrating neurological, endocrinal and immunological functions-are stored in secretory vesicles by vesicular monoamine transporters (VMATs) for controlled ...Biogenic monoamines-vital transmitters orchestrating neurological, endocrinal and immunological functions-are stored in secretory vesicles by vesicular monoamine transporters (VMATs) for controlled quantal release. Harnessing proton antiport, VMATs enrich monoamines around 10,000-fold and sequester neurotoxicants to protect neurons. VMATs are targeted by an arsenal of therapeutic drugs and imaging agents to treat and monitor neurodegenerative disorders, hypertension and drug addiction. However, the structural mechanisms underlying these actions remain unclear. Here we report eight cryo-electron microscopy structures of human VMAT1 in unbound form and in complex with four monoamines (dopamine, noradrenaline, serotonin and histamine), the Parkinsonism-inducing MPP, the psychostimulant amphetamine and the antihypertensive drug reserpine. Reserpine binding captures a cytoplasmic-open conformation, whereas the other structures show a lumenal-open conformation stabilized by extensive gating interactions. The favoured transition to this lumenal-open state contributes to monoamine accumulation, while protonation facilitates the cytoplasmic-open transition and concurrently prevents monoamine binding to avoid unintended depletion. Monoamines and neurotoxicants share a binding pocket that possesses polar sites for specificity and a wrist-and-fist shape for versatility. Variations in this pocket explain substrate preferences across the SLC18 family. Overall, these structural insights and supporting functional studies elucidate the mechanism of vesicular monoamine transport and provide the basis to develop therapeutics for neurodegenerative diseases and substance abuse. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41238.map.gz | 110.5 MB | EMDB map data format | |
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Header (meta data) | emd-41238-v30.xml emd-41238.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41238_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_41238.png | 123.9 KB | ||
Filedesc metadata | emd-41238.cif.gz | 5.8 KB | ||
Others | emd_41238_half_map_1.map.gz emd_41238_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41238 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41238 | HTTPS FTP |
-Validation report
Summary document | emd_41238_validation.pdf.gz | 723.2 KB | Display | EMDB validaton report |
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Full document | emd_41238_full_validation.pdf.gz | 722.8 KB | Display | |
Data in XML | emd_41238_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_41238_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41238 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41238 | HTTPS FTP |
-Related structure data
Related structure data | 8tgjMC 8tggC 8tghC 8tgiC 8tgkC 8tglC 8tgmC 8tgnC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41238.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | VMAT1 dimer in unbound form and with reserpine | ||||||||||||||||||||||||||||||||||||
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
-Half map: VMAT1 dimer in unbound form and with reserpine
File | emd_41238_half_map_1.map | ||||||||||||
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Annotation | VMAT1 dimer in unbound form and with reserpine | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: VMAT1 dimer in unbound form and with reserpine
File | emd_41238_half_map_2.map | ||||||||||||
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Annotation | VMAT1 dimer in unbound form and with reserpine | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of VMAT1 dimer in unbound form and with reserpine
Entire | Name: Complex of VMAT1 dimer in unbound form and with reserpine |
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Components |
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-Supramolecule #1: Complex of VMAT1 dimer in unbound form and with reserpine
Supramolecule | Name: Complex of VMAT1 dimer in unbound form and with reserpine type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 105.2 KDa |
-Macromolecule #1: VMAT1 dimer in unbound form and with reserpine
Macromolecule | Name: VMAT1 dimer in unbound form and with reserpine / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.565641 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MLRTILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS LHLGHAGSNC LQGTGFLEEE ITRVGVLFA SKAVMQLLVN PFVGPLTNRI GYHIPMFAGF VIMFLSTVMF AFSGTYTLLF VARTLQGIGS SFSSVAGLGM L ASVYTDDH ...String: MLRTILDAPQ RLLKEGRASR QLVLVVVFVA LLLDNMLFTV VVPIVPTFLY DMEFKEVNSS LHLGHAGSNC LQGTGFLEEE ITRVGVLFA SKAVMQLLVN PFVGPLTNRI GYHIPMFAGF VIMFLSTVMF AFSGTYTLLF VARTLQGIGS SFSSVAGLGM L ASVYTDDH ERGRAMGTAL GGLALGLLVG APFGSVMYEF VGKSAPFLIL AFLALLDGAL QLCILQPSKV SPESAKGTPL FM LLKDPYI LVAAGSICFA NMGVAILEPT LPIWMMQTMC SPKWQLGLAF LPASVSYLIG TNLFGVLANK MGRWLCSLIG MLV VGTSLL CVPLAHNIFG LIGPNAGLGL AIGMVDSSMM PIMGHLVDLR HTSVYGSVYA IADVAFCMGF AIGPSTGGAI VKAI GFPWL MVITGVINIV YAPLCYYLRS PPAKEEKLAI LSQDCPMETR MYATQKPTKE FPLGEDSDEE PDHEE |
-Macromolecule #2: reserpine
Macromolecule | Name: reserpine / type: ligand / ID: 2 / Number of copies: 1 / Formula: YHR |
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Molecular weight | Theoretical: 608.679 Da |
Chemical component information | ChemComp-YHR: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Temperature | Min: 63.0 K / Max: 77.2 K |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4301 / Average exposure time: 9.36 sec. / Average electron dose: 47.88 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 150000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |