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- PDB-5wen: GluA2 bound to GSG1L in digitonin, state 2 -

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Basic information

Entry
Database: PDB / ID: 5wen
TitleGluA2 bound to 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 (6.8 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: Glutamate receptor 2,Germ cell-specific gene 1-like protein
B: Glutamate receptor 2,Germ cell-specific gene 1-like protein
C: Glutamate receptor 2,Germ cell-specific gene 1-like protein
D: Glutamate receptor 2,Germ cell-specific gene 1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,3436
Polyers469,8854
Non-polymers2,4592
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)26160
ΔGint (kcal/M)-184
Surface area (Å2)161020

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Components

#1: Polypeptide(L)
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 residues 25-847 and UNP residues 2-238 linked via LINKER GTG,UNP residues 25-847 and UNP residues 2-238 linked via LINKER GTG
Mutation: N241E, V382L, G384E, N385D, N392Q, V1151L,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: ChemicalChemComp-AJP / Digitonin


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

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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 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 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

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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: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18926 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00327952
ELECTRON MICROSCOPYf_angle_d0.80337796
ELECTRON MICROSCOPYf_dihedral_angle_d10.07616522
ELECTRON MICROSCOPYf_chiral_restr0.0474220
ELECTRON MICROSCOPYf_plane_restr0.0074752

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