[English] 日本語
Yorodumi
- EMDB-25666: Rat vesicular glutamate transporter 2 (VGLUT2) in low Cl condition -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25666
TitleRat vesicular glutamate transporter 2 (VGLUT2) in low Cl condition
Map datasharpened map for model building
Sample
  • Complex: complex of WT VGLUT2 with a Fab
    • Protein or peptide: Vesicular glutamate transporter 2
Keywordssynaptic vesicle / neurotransmitter / glutamate transport / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium:phosphate symporter activity / sodium-dependent phosphate transport / L-glutamate uniporter activity / phosphate ion uniporter activity / pericellular basket / Organic anion transport by SLC5/17/25 transporters / neurotransmitter uptake / hyaloid vascular plexus regression / L-glutamate import / neurotransmitter loading into synaptic vesicle ...sodium:phosphate symporter activity / sodium-dependent phosphate transport / L-glutamate uniporter activity / phosphate ion uniporter activity / pericellular basket / Organic anion transport by SLC5/17/25 transporters / neurotransmitter uptake / hyaloid vascular plexus regression / L-glutamate import / neurotransmitter loading into synaptic vesicle / L-glutamate transmembrane transporter activity / potassium:proton antiporter activity / L-glutamate transmembrane transport / phosphate ion homeostasis / neurotransmitter transmembrane transporter activity / phosphate ion transport / neural retina development / regulation of synapse structure or activity / chloride channel activity / excitatory synapse / chloride channel complex / synaptic transmission, glutamatergic / hippocampus development / synaptic vesicle / synaptic vesicle membrane / presynapse / early endosome / neuron projection / plasma membrane
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Vesicular glutamate transporter 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi F / Stroud RM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS089713 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)K99MH119591 United States
CitationJournal: To Be Published
Title: Substrate Recognition, Directional Flux, and Allostery in a Synaptic Vesicle Glutamate Transporter
Authors: Li F / Stroud RM
History
DepositionDec 8, 2021-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25666.png

Downloads & links

-
Map

FileDownload / File: emd_25666.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.1
Minimum - Maximum-39.436999999999998 - 55.372149999999998
Average (Standard dev.)0.000000000000121 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : complex of WT VGLUT2 with a Fab

EntireName: complex of WT VGLUT2 with a Fab
Components
  • Complex: complex of WT VGLUT2 with a Fab
    • Protein or peptide: Vesicular glutamate transporter 2

-
Supramolecule #1: complex of WT VGLUT2 with a Fab

SupramoleculeName: complex of WT VGLUT2 with a Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

-
Macromolecule #1: Vesicular glutamate transporter 2

MacromoleculeName: Vesicular glutamate transporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 64.63727 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MESVKQRILA PGKEGIKNFA GKSLGQIYRV LEKKQDNRET IELTEDGKPL EVPEKKAPLC DCTCFGLPRR YIIAIMSGLG FCISFGIRC NLGVAIVDMV NNSTIHRGGK VIKEKAKFNW DPETVGMIHG SFFWGYIITQ IPGGYIASRL AANRVFGAAI L LTSTLNML ...String:
MESVKQRILA PGKEGIKNFA GKSLGQIYRV LEKKQDNRET IELTEDGKPL EVPEKKAPLC DCTCFGLPRR YIIAIMSGLG FCISFGIRC NLGVAIVDMV NNSTIHRGGK VIKEKAKFNW DPETVGMIHG SFFWGYIITQ IPGGYIASRL AANRVFGAAI L LTSTLNML IPSAARVHYG CVIFVRILQG LVEGVTYPAC HGIWSKWAPP LERSRLATTS FCGSYAGAVI AMPLAGILVQ YT GWSSVFY VYGSFGMVWY MFWLLVSYES PAKHPTITDE ERRYIEESIG ESANLLGAME KFKTPWRKFF TSMPVYAIIV ANF CRSWTF YLLLISQPAY FEEVFGFEIS KVGMLSAVPH LVMTIIVPIG GQIADFLRSK QILSTTTVRK IMNCGGFGME ATLL LVVGY SHTRGVAISF LVLAVGFSGF AISGFNVNHL DIAPRYASIL MGISNGVGTL SGMVCPIIVG AMTKNKSREE WQYVF LIAA LVHYGGVIFY ALFASGEKQP WADPEETSEE KCGFIHEDEL DEETGDITQN YINYGTTKSY GATSQENGGW PNGWEK KEE FVQESAQDAY SYKDRDDYS

UniProtKB: Vesicular glutamate transporter 2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6v4d
PDB Unreleased entry

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152461
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6v4d
PDB Unreleased entry


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7t3o:
Rat vesicular glutamate transporter 2 (VGLUT2) in low Cl condition

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more