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Yorodumi- EMDB-41269: Structure of the human vesicular monoamine transporter 2 (VMAT2) ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41269 | |||||||||
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Title | Structure of the human vesicular monoamine transporter 2 (VMAT2) bound to Tetrabenazine in an occluded conformation | |||||||||
Map data | DeepEMhancer sharpened with local mask | |||||||||
Sample |
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Keywords | monoamine / neurotransmitter / synaptic vesicles / major facilitator superfamily / SLC18 / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information serotonin secretion by mast cell / sequestering of neurotransmitter / somato-dendritic dopamine secretion / histamine uptake / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / aminergic neurotransmitter loading into synaptic vesicle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity ...serotonin secretion by mast cell / sequestering of neurotransmitter / somato-dendritic dopamine secretion / histamine uptake / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / aminergic neurotransmitter loading into synaptic vesicle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / serotonin uptake / dopaminergic synapse / dopamine transport / monoamine transmembrane transporter activity / Na+/Cl- dependent neurotransmitter transporters / monoamine transport / histamine secretion by mast cell / neurotransmitter transport / negative regulation of reactive oxygen species biosynthetic process / response to amphetamine / post-embryonic development / secretory granule membrane / locomotory behavior / terminal bouton / response to toxic substance / synaptic vesicle membrane / synaptic vesicle / chemical synaptic transmission / axon / intracellular membrane-bounded organelle / centrosome / dendrite / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Vicugna pacos (alpaca) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||
Authors | Dalton MP / Coleman JA | |||||||||
Funding support | 1 items
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Citation | Journal: Elife / Year: 2024 Title: Structural mechanisms for VMAT2 inhibition by tetrabenazine. Authors: Michael P Dalton / Mary Hongying Cheng / Ivet Bahar / Jonathan A Coleman / Abstract: The vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several ...The vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several neuropsychiatric disorders including Parkinson's disease and schizophrenia. Furthermore, drugs such as amphetamine and MDMA are known to act on VMAT2, exemplifying its role in the mechanisms of actions for drugs of abuse. Despite VMAT2's importance, there remains a critical lack of mechanistic understanding, largely driven by a lack of structural information. Here, we report a 3.1 Å resolution cryo-electron microscopy (cryo-EM) structure of VMAT2 complexed with tetrabenazine (TBZ), a non-competitive inhibitor used in the treatment of Huntington's chorea. We find TBZ interacts with residues in a central binding site, locking VMAT2 in an occluded conformation and providing a mechanistic basis for non-competitive inhibition. We further identify residues critical for cytosolic and lumenal gating, including a cluster of hydrophobic residues which are involved in a lumenal gating strategy. Our structure also highlights three distinct polar networks that may determine VMAT2 conformational dynamics and play a role in proton transduction. The structure elucidates mechanisms of VMAT2 inhibition and transport, providing insights into VMAT2 architecture, function, and the design of small-molecule therapeutics. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41269.map.gz | 195.8 MB | EMDB map data format | |
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Header (meta data) | emd-41269-v30.xml emd-41269.xml | 21 KB 21 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41269_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_41269.png | 63.6 KB | ||
Masks | emd_41269_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-41269.cif.gz | 6.8 KB | ||
Others | emd_41269_additional_1.map.gz emd_41269_additional_2.map.gz emd_41269_half_map_1.map.gz emd_41269_half_map_2.map.gz | 107.2 MB 193.6 MB 200.7 MB 200.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41269 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41269 | HTTPS FTP |
-Validation report
Summary document | emd_41269_validation.pdf.gz | 881.9 KB | Display | EMDB validaton report |
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Full document | emd_41269_full_validation.pdf.gz | 881.4 KB | Display | |
Data in XML | emd_41269_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | emd_41269_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41269 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41269 | HTTPS FTP |
-Related structure data
Related structure data | 8thrMC 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_41269.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | DeepEMhancer sharpened with local mask | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.647 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41269_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: unsharpened map
File | emd_41269_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
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Density Histograms |
-Additional map: DeepEMhancer sharpened with a solvent mask
File | emd_41269_additional_2.map | ||||||||||||
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Annotation | DeepEMhancer sharpened with a solvent mask | ||||||||||||
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Density Histograms |
-Half map: half map A
File | emd_41269_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_41269_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
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Density Histograms |
-Sample components
-Entire : Human VMAT2 complexed with Tetrabenazine
Entire | Name: Human VMAT2 complexed with Tetrabenazine |
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Components |
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-Supramolecule #1: Human VMAT2 complexed with Tetrabenazine
Supramolecule | Name: Human VMAT2 complexed with Tetrabenazine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 93.7 KDa |
-Macromolecule #1: fluorescent protein mVenus,Synaptic vesicular amine transporter,G...
Macromolecule | Name: fluorescent protein mVenus,Synaptic vesicular amine transporter,GFP nano body,Synaptic vesicular amine transporter,Synaptic vesicular amine transporter type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Molecular weight | Theoretical: 93.85093 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MWSHPQFEKG GGSGGGSGGS AWSHPQFEKH HHHHHHHHHG SGVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKLI CTTGKLPVPW PTLVTTLGYG LQCFARYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD T LVNRIELK ...String: MWSHPQFEKG GGSGGGSGGS AWSHPQFEKH HHHHHHHHHG SGVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKLI CTTGKLPVPW PTLVTTLGYG LQCFARYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD T LVNRIELK GIDFKEDGNI LGHKLEYNYN SHNVYITADK QKNGIKANFK IRHNIEDGGV QLADHYQQNT PIGDGPVLLP DN HYLSYQS KLSKDPNEKR DHMVLLEFVT AAGITLGMDE LYKSRKLILF IVFLALLLDN MLLTVVVPII PSYLYSIKHE KNA TEIQTA RPVHTASISD SFQSIFSYYD NSTMVTGNAT RDLTLHQTAT QHMVTNASAV PSDCPSEDKD LLNENVQVGL LFAS KATVQ LITNPFIGLL TNRIGYPIPI FAGFCIMFVS TIMFAFSSSY AFLLIARSLQ GIGSSCSSVA GMGMLASVYT DDEER GNVM GIALGGLAMG VLVGPPFGSV LYEFVGKTAP FLVLAALVLL DGAIQLFVLQ PSRVQPESQK GTPLTTLLKD PYILIA AGS ICFANMGIAM LEPALPIWMM ETMCSRKWQL GVAFLPASIS YLIGTNIFGI LAHKMGRWLC ALLGMIIVGV SILCIPF AK NIYGLIAPNF GVGFAIGMVD SSMMPIMGYL VDLRHVSVYG SVYAIADVAF CMGYAIGPSA GGAIAKAIGF PWLMTIIG I IDILFAPLCF FLRSPPAKEE KMAIVQLVES GGALVQPGGS LRLSCAASGF PVNRYSMRWY RQAPGKEREW VAGMSSAGD RSSYEDSVKG RFTISRDDAR NTVYLQMNSL KPEDTAVYYC NVNVGFEYWG QGTQVTVS UniProtKB: Synaptic vesicular amine transporter |
-Macromolecule #2: (3S,5R,11bS)-9,10-dimethoxy-3-(2-methylpropyl)-1,3,4,6,7,11b-hexa...
Macromolecule | Name: (3S,5R,11bS)-9,10-dimethoxy-3-(2-methylpropyl)-1,3,4,6,7,11b-hexahydro-2H-pyrido[2,1-a]isoquinolin-2-one type: ligand / ID: 2 / Number of copies: 1 / Formula: EBZ |
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Molecular weight | Theoretical: 317.423 Da |
Chemical component information | ChemComp-EBZ: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL |
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Buffer | pH: 8 Details: 1 mM DDM, .125 mM CHS, 1 mM DTT, 100 uM TBZ, 25 mM Tris HCl pH 8, 150 mM NaCl |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 77279 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |