+Open data
-Basic information
Entry | Database: PDB / ID: 8xiu | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of a frog VMAT2 in an apo conformation | ||||||
Components | XlVMAT2 | ||||||
Keywords | TRANSPORT PROTEIN / Vesicular monoamine transporter / SLC18A2 / MFS / fold | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Lyu, Y. / Fu, C. / Ma, H. / Sun, Z. / Su, Z. / Zhou, X. | ||||||
Funding support | China, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8xiu.cif.gz | 71.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8xiu.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 8xiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xiu_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8xiu_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8xiu_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 8xiu_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/8xiu ftp://data.pdbj.org/pub/pdb/validation_reports/xi/8xiu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 55624.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Komagataella pastoris (fungus) |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: XlVMAT2 WT / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Source (recombinant) | Organism: Komagataella pastoris (fungus) |
Buffer solution | pH: 6 / Details: 150 mm NaCl, 20 mM MES-Na pH 6.0, 0.4 mM DDM |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 3 s before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 900 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107961 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||
Refine LS restraints |
|