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- PDB-5wek: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 1 -

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Entry
Database: PDB / ID: 5wek
TitleGluA2 bound to antagonist ZK and GSG1L in digitonin, state 1
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 (4.6 Å resolution / Particle / Single particle)
AuthorsTwomey, E.C. / Yelshanskaya, M.V. / Grassucci, R.A. / Frank, J. / Sobolevsky, A.I.
CitationNature, 2017, 549, 60-65

Nature, 2017, 549, 60-65 Yorodumi Papers
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
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

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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)471,5228
Polyers469,8854
Non-polymers1,6374
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)28520
ΔGint (kcal/M)-209
Surface area (Å2)159320

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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

Cellular component

Molecular function

Biological process

#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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 1
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 1
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

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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

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 26971 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00428068
ELECTRON MICROSCOPYf_angle_d0.85937976
ELECTRON MICROSCOPYf_dihedral_angle_d10.10916590
ELECTRON MICROSCOPYf_chiral_restr0.0474220
ELECTRON MICROSCOPYf_plane_restr0.0074760

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