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- EMDB-34076: GluK1-1a in nanodisc captured in SYM2081 bound desensitized state -

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Basic information

Entry
Database: EMDB / ID: EMD-34076
TitleGluK1-1a in nanodisc captured in SYM2081 bound desensitized state
Map dataGluK1-1a nanodisc captured in desensitized state
Sample
  • Complex: Complex of GluK1-1a in lipid nanodisc with SYM2081
    • Protein or peptide: Glutamate receptor
KeywordsKainate receptor / GluK1-1a splice variant / nanodisc / SYM2081 bound / desensitized state / MEMBRANE PROTEIN
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / signaling receptor activity / postsynaptic membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsDhingra S / Kumar J
Funding support India, 1 items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2020/003971 India
CitationJournal: Elife / Year: 2023
Title: Functional Implications of the Exon 9 Splice Insert in GluK1 Kainate Receptors
Authors: Dhingra S / Chopade PM / Vinnakota R / Kumar J
History
DepositionAug 12, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34076.png

Downloads & links

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Map

FileDownload / File: emd_34076.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluK1-1a nanodisc captured in desensitized state
Voxel sizeX=Y=Z: 1.41 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.00074294425 - 2.0170407
Average (Standard dev.)0.0049278038 (±0.055036537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 360.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: GluK1-1a nanodisc captured in desensitized state halfmap A

Fileemd_34076_half_map_1.map
AnnotationGluK1-1a nanodisc captured in desensitized state_halfmap_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GluK1-1a nanodisc captured in desensitized state halfmap B

Fileemd_34076_half_map_2.map
AnnotationGluK1-1a nanodisc captured in desensitized state_halfmap_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of GluK1-1a in lipid nanodisc with SYM2081

EntireName: Complex of GluK1-1a in lipid nanodisc with SYM2081
Components
  • Complex: Complex of GluK1-1a in lipid nanodisc with SYM2081
    • Protein or peptide: Glutamate receptor

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Supramolecule #1: Complex of GluK1-1a in lipid nanodisc with SYM2081

SupramoleculeName: Complex of GluK1-1a in lipid nanodisc with SYM2081 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: EGFP is covalently conjugated to the C-terminus of GluK1-1a. MSP1E3D1 soybean polar lipid nanodisc used.
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: Glutamate receptor

MacromoleculeName: Glutamate receptor / type: protein_or_peptide / ID: 1
Details: L838-S843 correspond to Thrombin recognition site, A844-A847 correspond to Ala linker, V848-S1090 correspond to enhanced green fluorescent protein (EGFP), H1091-H1098 correspond to Octa-His affinity tag.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 124.527125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVLRIGGIFE TVENEPVNVE ELAFKFAVTS INRNRTLMPN TTLTYDIQRI NLFDSFEASR RACDQLALGV AALFGPSHSS SVSAVQSIC NALEVPHIQT RWKHPSVDSR DLFYINLYPD YAAISRAVLD LVLYYNWKTV TVVYEDSTGL IRLQELIKAP S RYNIKIKI ...String:
QVLRIGGIFE TVENEPVNVE ELAFKFAVTS INRNRTLMPN TTLTYDIQRI NLFDSFEASR RACDQLALGV AALFGPSHSS SVSAVQSIC NALEVPHIQT RWKHPSVDSR DLFYINLYPD YAAISRAVLD LVLYYNWKTV TVVYEDSTGL IRLQELIKAP S RYNIKIKI RQLPPANKDA KPLLKEMKKS KEFYVIFDCS HETAAEILKQ ILFMGMMTEY YHYFFTTLDL FALDLELYRY SG VNMTGFR LLNIDNPHVS SIIEKWSMER LQAPPRPETG LLDGMMTTEA ALMYDAVYMV AIASHRASQL TVSSLQCHRH KPW RLGPRF MNLIKEARWD GLTGRITFNK TDGLRKDFDL DIISLKEEGT EKASGEVSKH LYKVWKKIGI WNSNSGLNMT DGNR DRSNN ITDSLANRTL IVTTILEEPY VMYRKSDKPL YGNDRFEGYC LDLLKELSNI LGFLYDVKLV PDGKYGAQND KGEWN GMVK ELIDHRADLA VAPLTITYVR EKVIDFSKPF MTLGISILYR KPNGTNPGVF SFLNPLSPDI WMYVLLAYLG VSVVLF VIA RFTPYEWYNP HPCNPDSDVV ENNFTLLNSF WFGVGALMQQ GSELMPKALS TRIVGGIWWF FTLIIISSYT ANLAAFL TV ERMESPIDSA DDLAKQTKIE YGAVRDGSTM TFFKKSKIST YEKMWAFMSS RQQSALVKNS DEGIQRVLTT DYALLMES T SIEYVTQRNC NLTQIGGLID SKGYGVGTPI GSPYRDKITI AILQLQEEGK LHMMKEKWWR GNGCPEEDSK EASALGVEN IGGIFIVLAA GLVLSVFVAI GEFLYKSRKN NDVEQHYLVP RGSAAAAVSK GEELFTGVVP ILVELDGDVN GHKFSVSGEG EGDATYGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKQHD FFKSAMPEGY VQERTIFFKD DGNYKTRAEV K FEGDTLVN RIELKGIDFK EDGNILGHKL EYNYNSHNVY IMADKQKNGI KVNFKIRHNI EDGSVQLADH YQQNTPIGDG PV LLPDNHY LSTQSKLSKD PNEKRDHMVL LEFVTAAGIT LGMDELYKSG LRSHHHHHHH H

UniProtKB: Glutamate receptor

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.87 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 12.0 sec. / Average electron dose: 40.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5kuf


Details: Unpublished coordinates for the amino-terminal domain model 3C32 used for ligand binding domain model 5KUF used for the trans-membrane domain model
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24531

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Atomic model buiding 1

Initial model
PDB IDChain

3c32

source_name: PDB, initial_model_type: experimental model

5kuf

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7ysj:
GluK1-1a in nanodisc captured in SYM2081 bound desensitized state

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