[English] 日本語
Yorodumi
- PDB-7t3o: Rat vesicular glutamate transporter 2 (VGLUT2) in low Cl condition -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t3o
TitleRat vesicular glutamate transporter 2 (VGLUT2) in low Cl condition
ComponentsVesicular glutamate transporter 2
KeywordsTRANSPORT PROTEIN / synaptic vesicle / neurotransmitter / glutamate transport
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
: / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi, F. / Stroud, R.M. / Edwards, R.H.
Funding support United States, 2items
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, R.M.
History
DepositionDec 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vesicular glutamate transporter 2


Theoretical massNumber of molelcules
Total (without water)64,6371
Polymers64,6371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Vesicular glutamate transporter 2 / VGluT2 / Differentiation-associated BNPI / Differentiation-associated Na(+)-dependent inorganic ...VGluT2 / Differentiation-associated BNPI / Differentiation-associated Na(+)-dependent inorganic phosphate cotransporter / Solute carrier family 17 member 6


Mass: 64637.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc17a6, Dnpi, Vglut2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9JI12

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: complex of WT VGLUT2 with a Fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 20000 nm / Nominal defocus min: 5000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152461 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6V4D

6v4d
PDB Unreleased entry


Accession code: 6V4D / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0063507
ELECTRON MICROSCOPYf_angle_d0.6584780
ELECTRON MICROSCOPYf_dihedral_angle_d7.5071993
ELECTRON MICROSCOPYf_chiral_restr0.045539
ELECTRON MICROSCOPYf_plane_restr0.003595

+
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://pdbjlc1.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