+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38390 | |||||||||
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Title | Cryo-EM structure of a frog VMAT2 in an apo conformation | |||||||||
Map data | XlVMAT2 WT. | |||||||||
Sample |
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Keywords | Vesicular monoamine transporter / SLC18A2 / MFS / fold / TRANSPORT PROTEIN | |||||||||
Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Lyu Y / Fu C / Ma H / Sun Z / Su Z / Zhou X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Engineering of a mammalian VMAT2 for cryo-EM analysis results in non-canonical protein folding. Authors: Ying Lyu / Chunting Fu / Haiyun Ma / Zhaoming Su / Ziyi Sun / Xiaoming Zhou / Abstract: Vesicular monoamine transporter 2 (VMAT2) belongs to the major facilitator superfamily (MFS), and mediates cytoplasmic monoamine packaging into presynaptic vesicles. Here, we present two cryo-EM ...Vesicular monoamine transporter 2 (VMAT2) belongs to the major facilitator superfamily (MFS), and mediates cytoplasmic monoamine packaging into presynaptic vesicles. Here, we present two cryo-EM structures of VMAT2, with a frog VMAT2 adopting a canonical MFS fold and an engineered sheep VMAT2 adopting a non-canonical fold. Both VMAT2 proteins mediate uptake of a selective fluorescent VMAT2 substrate into cells. Molecular docking, substrate binding and transport analysis reveal potential substrate binding mechanism in VMAT2. Meanwhile, caution is advised when interpreting engineered membrane protein structures. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38390.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-38390-v30.xml emd-38390.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38390_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_38390.png | 85.7 KB | ||
Filedesc metadata | emd-38390.cif.gz | 5.7 KB | ||
Others | emd_38390_half_map_1.map.gz emd_38390_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38390 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38390 | HTTPS FTP |
-Validation report
Summary document | emd_38390_validation.pdf.gz | 945.2 KB | Display | EMDB validaton report |
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Full document | emd_38390_full_validation.pdf.gz | 944.9 KB | Display | |
Data in XML | emd_38390_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_38390_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38390 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38390 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_38390.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | XlVMAT2 WT. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B.
File | emd_38390_half_map_1.map | ||||||||||||
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Annotation | Half map B. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A.
File | emd_38390_half_map_2.map | ||||||||||||
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Annotation | Half map A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : XlVMAT2 WT
Entire | Name: XlVMAT2 WT |
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Components |
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-Supramolecule #1: XlVMAT2 WT
Supramolecule | Name: XlVMAT2 WT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
-Macromolecule #1: XlVMAT2
Macromolecule | Name: XlVMAT2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 55.624984 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MSMTEFTLLR WLREGRQSRK LILLIVFIAL LLDNMLLTVV VPIIPSYLYS MTHESNNTHD GSIPPAAPSG FHSIFSYYDN TTVITTNFT SSDQLQQSAL TPTTSPSLAT PPASADCPKA DSSLLNENVK VGLLFASKAT VQLLTNPFIG PMTNRIGYQI P MFAGFCIM ...String: MSMTEFTLLR WLREGRQSRK LILLIVFIAL LLDNMLLTVV VPIIPSYLYS MTHESNNTHD GSIPPAAPSG FHSIFSYYDN TTVITTNFT SSDQLQQSAL TPTTSPSLAT PPASADCPKA DSSLLNENVK VGLLFASKAT VQLLTNPFIG PMTNRIGYQI P MFAGFCIM FVSTIMFAFS GTYTLLFIAR SLQGIGSSCS SVAGMGMLAS VYTDDEERGN AMGVALGGLA MGVLVGPPFG SI LYEFVGK TAPFIVLAVL VLFDGALQLF VLQPSRVQPE SQTGTPLLTL IRDPYILIAA GSICFANMAI AMLEPALPIW MME TMCSRK WQLGVAFLPA SISYLLGTNI FGPLAHKMGR WLCAFIGMIM VGISIICVPF ARNIYGLIAP NFGVGFAIGM VDSS MMPIM GYLVDLRHVS VYGSVYAIAD VAFCMGFAFG PSAGGAIAKS IGFPWLMTII GVVDILFAPL CLFLRSPPAR EEKMA ILMD HKCPVKTKMY TQNSGQPYYT GEEEESESDE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8.0 mg/mL |
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Buffer | pH: 6 / Details: 150 mm NaCl, 20 mM MES-Na pH 6.0, 0.4 mM DDM |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 s before plunging. |
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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 / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.9 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | PDB-8xiu: |