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- PDB-5weo: Activated GluA2 complex bound to glutamate, cyclothiazide, and ST... -

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Basic information

Entry
Database: PDB / ID: 5weo
TitleActivated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
DescriptorGlutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
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 (4.2 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

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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

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Components

#1: Polypeptide(L)
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 / 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: O88602
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Mass: 147.129 Da / Num. of mol.: 4 / Formula: C5H9NO4
#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

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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: 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
Source (recombinant)Cell: HEK293 gnti- / Organism: Homo sapiens
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

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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 FIELD
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

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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: 4.2 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

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