[English] 日本語
Yorodumi
- PDB-5weo: Activated GluA2 complex bound to glutamate, cyclothiazide, and ST... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5weo
TitleActivated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
ComponentsGlutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
KeywordsTRANSPORT PROTEIN / Ion channel
Function / homologyVoltage-dependent calcium channel, gamma-2 subunit / Presynaptic depolarization and calcium channel opening / PMP-22/EMP/MP20/Claudin superfamily / Receptor, ligand binding region / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Voltage-dependent calcium channel, gamma subunit / Ligand-gated ion channel / PMP-22/EMP/MP20/Claudin family ...Voltage-dependent calcium channel, gamma-2 subunit / Presynaptic depolarization and calcium channel opening / PMP-22/EMP/MP20/Claudin superfamily / Receptor, ligand binding region / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Voltage-dependent calcium channel, gamma subunit / Ligand-gated ion channel / PMP-22/EMP/MP20/Claudin family / Receptor family ligand binding region / Ligated ion channel L-glutamate- and glycine-binding site / Periplasmic binding protein-like I / Phase 2 - plateau phase / Trafficking of AMPA receptors / Phase 0 - rapid depolarisation / LGI-ADAM interactions / positive regulation of protein localization to basolateral plasma membrane / eye blink reflex / neurotransmitter receptor transport, postsynaptic endosome to lysosome / cerebellar mossy fiber / channel regulator activity / neurotransmitter receptor internalization / regulation of postsynaptic membrane neurotransmitter receptor levels / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of AMPA receptor activity / regulation of AMPA receptor activity / regulation of postsynaptic neurotransmitter receptor activity / postsynaptic neurotransmitter receptor diffusion trapping / membrane hyperpolarization / voltage-gated calcium channel complex / somatodendritic compartment / protein targeting to membrane / neuromuscular junction development / membrane depolarization / transmission of nerve impulse / nervous system process / postsynaptic density membrane / voltage-gated calcium channel activity / AMPA glutamate receptor activity / asymmetric synapse / ionotropic glutamate receptor binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / response to lithium ion / regulation of receptor recycling / positive regulation of synaptic transmission, glutamatergic / SNARE binding / positive regulation of synaptic transmission / integral component of postsynaptic membrane / regulation of membrane potential / regulation of synaptic transmission, glutamatergic / response to fungicide / integral component of postsynaptic density membrane / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / ionotropic glutamate receptor activity / ionotropic glutamate receptor signaling pathway / cytoskeletal protein binding / dendritic shaft / hippocampal mossy fiber to CA3 synapse / dendrite cytoplasm / receptor internalization / synaptic vesicle membrane / integral component of presynaptic membrane / PDZ domain binding / Schaffer collateral - CA1 synapse / presynaptic membrane / terminal bouton / response to calcium ion / establishment of protein localization / protein tetramerization / growth cone / chemical synaptic transmission / amyloid-beta binding / ATPase binding / perikaryon / signaling receptor activity / dendritic spine / postsynaptic density / cell junction / synapse / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / neuronal cell body / protein kinase binding / integral component of plasma membrane / cell surface / protein-containing complex / identical protein binding / plasma membrane / cytosol / Voltage-dependent calcium channel gamma-2 subunit / Glutamate receptor 2
Function and homology information
Specimen sourceRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsTwomey, E.C. / Yelshanskaya, M.V. / Grassucci, R.A. / Frank, J. / Sobolevsky, A.I.
CitationJournal: Nature / Year: 2017
Title: Channel opening and gating mechanism in AMPA-subtype glutamate receptors.
Authors: Edward C Twomey / Maria V Yelshanskaya / Robert A Grassucci / Joachim Frank / Alexander I Sobolevsky
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2017 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Sep 13, 2017Structure modelAuthor supporting evidence / Database referencescitation / pdbx_audit_support_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
1.2Jul 18, 2018Structure modelData collection / Experimental preparationem_sample_support_em_sample_support.grid_type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8823
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
B: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
C: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
D: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,15612
Polyers462,0084
Non-polymers2,1488
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)30380
ΔGint (kcal/M)-237
Surface area (Å2)191300

-
Components

#1: Protein/peptide
Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / Neuronal voltage-gated calcium channel gamma-2 subunit / Stargazin / Transmembrane AMPAR regulatory protein gamma-2 / TARP gamma-2


Mass: 115501.969 Da / Num. of mol.: 4
Fragment: UNP P19491 residues 25-847, UNP O88602 2-208 linked via LINKER GT
Mutation: N241E, V382L, G384E, N385D, V758L
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse)
Gene: Gria2, Glur2, Cacng2, Stg / Cell line (production host): HEK293 gnti- / Production host: Homo sapiens (human) / References: UniProt: P19491, UniProt: O88602
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Mass: 147.129 Da / Num. of mol.: 4 / Formula: C5H9NO4 / Glutamic acid
#3: Chemical
ChemComp-CYZ / CYCLOTHIAZIDE / 3-BICYCLO[2.2.1]HEPT-5-EN-2-YL-6-CHLORO-3,4- DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE-7-SULFONAMIDE 1,1 DIOXIDE


Mass: 389.878 Da / Num. of mol.: 4 / Formula: C14H16ClN3O4S2 / Cyclothiazide

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Cell: HEK293 gnti- / Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 4 mg/ml
Details: Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 8 sec. / Electron dose: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

-
Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 69207
Details: TMD map uploaded under additional files is at 4.0 angstrom resolution.
Symmetry type: POINT
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00831856
ELECTRON MICROSCOPYf_angle_d0.97743066
ELECTRON MICROSCOPYf_dihedral_angle_d10.88718730
ELECTRON MICROSCOPYf_chiral_restr0.0554774
ELECTRON MICROSCOPYf_plane_restr0.0075408

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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