[English] 日本語
Yorodumi
- PDB-5wel: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5wel
TitleGluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
DescriptorGlutamate receptor 2,Germ cell-specific gene 1-like protein
KeywordsTRANSPORT PROTEIN / Ion channel
Specimen sourceRattus norvegicus / mammal / Rat / ドブネズミ, どぶねずみ /
Mus musculus / mammal / Mouse / ハツカネズミ, はつかねずみ /
MethodElectron microscopy (4.4 Å resolution / Particle / Single particle)
AuthorsTwomey, E.C. / Yelshanskaya, M.V. / Grassucci, R.A. / Frank, J. / Sobolevsky, A.I.
CitationNature, 2017

Nature, 2017 StrPapers
Channel opening and gating mechanism in AMPA-subtype glutamate receptors.
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: Chimera of Glutamate receptor 2, Germ cell-specific gene 1-like protein
B: Chimera of Glutamate receptor 2, Germ cell-specific gene 1-like protein
C: Chimera of Glutamate receptor 2, Germ cell-specific gene 1-like protein
D: Chimera of Glutamate receptor 2, Germ cell-specific gene 1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)473,98010
Polyers469,8854
Non-polymers4,0966
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)26600
ΔGint (kcal/M)-200
Surface area (Å2)160520

-
Components

#1: Polypeptide(L)
Chimera of Glutamate receptor 2, Germ cell-specific gene 1-like protein / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / GSG1-like protein


Mass: 117471.211 Da / Num. of mol.: 4
Fragment: UNP P19491 residues 25-847, UNP D3Z7H4 residues 2-238 linked via LINKER GTG
Mutation: N241E, V382L, G384E, N385D, N392Q, V1151L
Source: (gene. exp.) Rattus norvegicus / mammal / ドブネズミ, どぶねずみ / , (gene. exp.) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
References: UniProt: P19491, UniProt: D3Z7H4
#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: ChemicalChemComp-AJP / Digitonin


Mass: 1229.312 Da / Num. of mol.: 2 / Formula: C56H92O29

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus
Source (recombinant)Organism: Homo sapiens
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml
Details: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Gold-gold grids, hydrogen and oxygen glow discharge (20s, 10 watts, 6.4 sccm H2, 27.5 sccm O2)
Grid 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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 67 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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 41926 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00428068
ELECTRON MICROSCOPYf_angle_d0.87737976
ELECTRON MICROSCOPYf_dihedral_angle_d10.31716590
ELECTRON MICROSCOPYf_chiral_restr0.0484220
ELECTRON MICROSCOPYf_plane_restr0.0074760

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more