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Yorodumi- EMDB-21040: Structure of the rat vesicular glutamate transporter 2 determined... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21040 | ||||||||||||
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Title | Structure of the rat vesicular glutamate transporter 2 determined by single particle Cryo-EM | ||||||||||||
Map data | sharpened map for model building not for FSC calculation. FSC curves are calculated on unsharpened maps. | ||||||||||||
Sample |
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Function / homology | Function and homology information sodium:phosphate symporter activity / sodium-dependent phosphate transport / phosphate ion uniporter activity / L-glutamate uniporter activity / pericellular basket / Organic anion transporters / neurotransmitter uptake / neurotransmitter loading into synaptic vesicle / L-glutamate import / hyaloid vascular plexus regression ...sodium:phosphate symporter activity / sodium-dependent phosphate transport / phosphate ion uniporter activity / L-glutamate uniporter activity / pericellular basket / Organic anion transporters / neurotransmitter uptake / neurotransmitter loading into synaptic vesicle / L-glutamate import / hyaloid vascular plexus regression / phosphate ion transport / L-glutamate transmembrane transport / potassium:proton antiporter activity / L-glutamate transmembrane transporter activity / phosphate ion homeostasis / neurotransmitter transmembrane transporter activity / neural retina development / regulation of synapse structure or activity / monoatomic anion transport / chloride channel activity / chloride channel complex / excitatory synapse / synaptic transmission, glutamatergic / hippocampus development / synaptic vesicle membrane / synaptic vesicle / presynapse / early endosome / neuron projection / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Li F / Finer-Moore J / Eriksen J / Cheng Y / Edwards R / Stroud R | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Science / Year: 2020 Title: Ion transport and regulation in a synaptic vesicle glutamate transporter. Authors: Fei Li / Jacob Eriksen / Janet Finer-Moore / Roger Chang / Phuong Nguyen / Alisa Bowen / Alexander Myasnikov / Zanlin Yu / David Bulkley / Yifan Cheng / Robert H Edwards / Robert M Stroud / Abstract: Synaptic vesicles accumulate neurotransmitters, enabling the quantal release by exocytosis that underlies synaptic transmission. Specific neurotransmitter transporters are responsible for this ...Synaptic vesicles accumulate neurotransmitters, enabling the quantal release by exocytosis that underlies synaptic transmission. Specific neurotransmitter transporters are responsible for this activity and therefore are essential for brain function. The vesicular glutamate transporters (VGLUTs) concentrate the principal excitatory neurotransmitter glutamate into synaptic vesicles, driven by membrane potential. However, the mechanism by which they do so remains poorly understood owing to a lack of structural information. We report the cryo-electron microscopy structure of rat VGLUT2 at 3.8-angstrom resolution and propose structure-based mechanisms for substrate recognition and allosteric activation by low pH and chloride. A potential permeation pathway for chloride intersects with the glutamate binding site. These results demonstrate how the activity of VGLUTs can be coordinated with large shifts in proton and chloride concentrations during the synaptic vesicle cycle to ensure normal synaptic transmission. | ||||||||||||
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_21040.map.gz | 60 MB | EMDB map data format | |
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Header (meta data) | emd-21040-v30.xml emd-21040.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
Images | emd_21040.png | 88.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21040 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21040 | HTTPS FTP |
-Validation report
Summary document | emd_21040_validation.pdf.gz | 536.8 KB | Display | EMDB validaton report |
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Full document | emd_21040_full_validation.pdf.gz | 536.3 KB | Display | |
Data in XML | emd_21040_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_21040_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21040 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21040 | HTTPS FTP |
-Related structure data
Related structure data | 8sbeMC 6v4d 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_21040.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map for model building not for FSC calculation. FSC curves are calculated on unsharpened maps. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 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 : vesicular glutamate transporter 2 in complex with a high affinity fab
Entire | Name: vesicular glutamate transporter 2 in complex with a high affinity fab |
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Components |
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-Supramolecule #1: vesicular glutamate transporter 2 in complex with a high affinity fab
Supramolecule | Name: vesicular glutamate transporter 2 in complex with a high affinity fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: Vesicular glutamate transporter 2
Macromolecule | Name: Vesicular glutamate transporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 58.893008 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: METIELTEDG KPLEVPEKKA PLCDCTCFGL PRRYIIAIMS GLGFCISFGI RCNLGVAIVD MVNNSTIHRG GKVIKEKAKF NWDPETVGM IHGSFFWGYI ITQIPGGYIA SRLAANRVFG AAILLTSTLN MLIPSAARVH YGCVIFVRIL QGLVEGVTYP A CHGIWSKW ...String: METIELTEDG KPLEVPEKKA PLCDCTCFGL PRRYIIAIMS GLGFCISFGI RCNLGVAIVD MVNNSTIHRG GKVIKEKAKF NWDPETVGM IHGSFFWGYI ITQIPGGYIA SRLAANRVFG AAILLTSTLN MLIPSAARVH YGCVIFVRIL QGLVEGVTYP A CHGIWSKW APPLERSRLA TTSFCGSYAG AVIAMPLAGI LVQYTGWSSV FYVYGSFGMV WYMFWLLVSY ESPAKHPTIT DE ERRYIEE SIGESANLLG AMEKFKTPWR KFFTSMPVYA IIVANFCRSW TFYLLLISQP AYFEEVFGFE ISKVGMLSAV PHL VMTIIV PIGGQIADFL RSKQILSTTT VRKIMNCGGF GMEATLLLVV GYSHTRGVAI SFLVLAVGFS GFAISGFNVN HLDI APRYA SILMGISNGV GTLSGMVCPI IVGAMTKNKS REEWQYVFLI AALVHYGGVI FYALFASGEK QPWADPEETS EEKCG FIHE DELDEETGDI TQNYINYGTT KSYGATGRPL EVLFQGPHHH HHHHHHH |
-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: 7.4 / Details: 20 mM HEPES, 150 mM NaCl, pH 7.4 and 0.01% GDN |
Grid | Model: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 5704 / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 36000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1919729 |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 243615 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8sbe: |