+Open data
-Basic information
Entry | Database: PDB / ID: 8gpr | ||||||
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Title | GluK1-1a receptor captured in the desensitized state | ||||||
Components | Glutamate receptor | ||||||
Keywords | MEMBRANE PROTEIN / Kainate receptor | ||||||
Function / homology | Function and homology information ligand-gated monoatomic ion channel activity / signaling receptor activity / postsynaptic membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å | ||||||
Authors | Dhingra, S. / Kumar, J. | ||||||
Funding support | India, 1items
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Citation | Journal: Elife / Year: 2023 Title: Functional Implications of the Exon 9 Splice Insert in GluK1 Kainate Receptors Authors: Dhingra, S. / Chopade, P.M. / Vinnakota, R. / Kumar, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gpr.cif.gz | 519.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gpr.ent.gz | 427.3 KB | Display | PDB format |
PDBx/mmJSON format | 8gpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gpr_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8gpr_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8gpr_validation.xml.gz | 92.3 KB | Display | |
Data in CIF | 8gpr_validation.cif.gz | 136.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/8gpr ftp://data.pdbj.org/pub/pdb/validation_reports/gp/8gpr | HTTPS FTP |
-Related structure data
Related structure data | 34197MC 7ysjC 7ysvC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 95606.672 Da / Num. of mol.: 4 / Mutation: C552Y, C557V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1 / Plasmid: pEGBacMam / Cell line (production host): HEK293 GnTI negative / Production host: Homo sapiens (human) / References: UniProt: A0A0G2K830 Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: GluK1-1a receptor in complex with SYM2081 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.381 MDa / Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Homo sapiens (human) / Plasmid: pEGBacMam |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.57 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 60 sec. / Electron dose: 19.5 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 13750 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5372 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refine LS restraints |
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