[English] 日本語
Yorodumi
- PDB-5kbu: Cryo-EM structure of GluA2-2xSTZ complex at 7.8 Angstrom resolution -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5kbu
TitleCryo-EM structure of GluA2-2xSTZ complex at 7.8 Angstrom resolution
ComponentsGlutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
KeywordsTRANSPORT PROTEIN / Cryo-EM
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 / Trafficking of AMPA receptors / Phase 2 - plateau phase / LGI-ADAM interactions / Phase 0 - rapid depolarisation / positive regulation of protein localization to basolateral plasma membrane / eye blink reflex / neurotransmitter receptor transport, postsynaptic endosome to lysosome / channel regulator activity / cerebellar mossy fiber / neurotransmitter receptor internalization / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of AMPA receptor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / positive regulation of synaptic transmission, glutamatergic / SNARE binding / positive regulation of synaptic transmission / regulation of membrane potential / integral component of postsynaptic membrane / regulation of synaptic transmission, glutamatergic / response to fungicide / integral component of postsynaptic density membrane / ionotropic glutamate receptor activity / ionotropic glutamate receptor signaling pathway / cytoskeletal protein binding / synaptic vesicle membrane / dendritic shaft / hippocampal mossy fiber to CA3 synapse / dendrite cytoplasm / receptor internalization / 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 / 7.8 Å resolution
AuthorsTwomey, E.C. / Yelshanskaya, M.V. / Grassucci, R.A. / Frank, J. / Sobolevsky, A.I.
CitationJournal: Science / Year: 2016
Title: Elucidation of AMPA receptor-stargazin complexes by cryo-electron microscopy.
Authors: Edward C Twomey / Maria V Yelshanskaya / Robert A Grassucci / Joachim Frank / Alexander I Sobolevsky
Abstract: AMPA-subtype ionotropic glutamate receptors (AMPARs) mediate fast excitatory neurotransmission and contribute to high cognitive processes such as learning and memory. In the brain, AMPAR trafficking, ...AMPA-subtype ionotropic glutamate receptors (AMPARs) mediate fast excitatory neurotransmission and contribute to high cognitive processes such as learning and memory. In the brain, AMPAR trafficking, gating, and pharmacology is tightly controlled by transmembrane AMPAR regulatory proteins (TARPs). Here, we used cryo-electron microscopy to elucidate the structural basis of AMPAR regulation by one of these auxiliary proteins, TARP γ2, or stargazin (STZ). Our structures illuminate the variable interaction stoichiometry of the AMPAR-TARP complex, with one or two TARP molecules binding one tetrameric AMPAR. Analysis of the AMPAR-STZ binding interfaces suggests that electrostatic interactions between the extracellular domains of AMPAR and STZ play an important role in modulating AMPAR function through contact surfaces that are conserved across AMPARs and TARPs. We propose a model explaining how TARPs stabilize the activated state of AMPARs and how the interactions between AMPARs and their auxiliary proteins control fast excitatory synaptic transmission.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 3, 2016 / Release: Jul 13, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 13, 2016Structure modelrepositoryInitial release
1.1Jul 20, 2016Structure modelOther
1.2Sep 27, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8231
  • 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
B: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
C: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
D: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,58612
Polyers462,0644
Non-polymers2,5228
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein/peptide
Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit / 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: 115515.984 Da / Num. of mol.: 4 / Mutation: N241E, V382L, G384E, N385D, V758L
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse)
Gene: Gria2, Glur2, Cacng2, Stg / Production host: Homo sapiens (human) / References: UniProt: P19491, UniProt: O88602
#2: Chemical
ChemComp-ZK1 / {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / [[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid


Mass: 409.254 Da / Num. of mol.: 4 / Formula: C14H15F3N3O6P
#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine
Compound detailsThe protein was expressed as a tandem fusion construct (GluA2 fused to stargazin, also named ...The protein was expressed as a tandem fusion construct (GluA2 fused to stargazin, also named TARP-y2 or cagcn2). However, this second protein which is covalently linked or fused to the C-terminus of GluA2 is not observed in chains B and D in this structure.

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Protein / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Cell: HEK293 / Organism: Homo sapiens (human) / Plasmid: Bacmam
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Grid coated with gold prior to use. / Grid material: GOLD / Grid mesh size: 200 / Grid type: C-flat Au 1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 kelvins / Details: 3 blot force, 8.0 s blot time

-
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
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 80 e/Å2
Details: 40 frames were collected across 8 seconds per image.
Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1
Image scansMovie frames/image: 40 / Used frames/image: 1-40

-
Processing

EM software
IDNameVersionCategory
1SerialEMimage acquisition
3CTFFIND4CTF correction
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 10293 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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