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- EMDB-34197: GluK1-1a receptor captured in the desensitized state -

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Basic information

Entry
Database: EMDB / ID: EMD-34197
TitleGluK1-1a receptor captured in the desensitized state
Map dataGluK1-1a captured in the desensitized state
Sample
  • Complex: GluK1-1a receptor in complex with SYM2081
    • Protein or peptide: Glutamate receptor
KeywordsKainate receptor / 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 / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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: 8.2 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 26, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34197.png

Downloads & links

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Map

FileDownload / File: emd_34197.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluK1-1a captured in the desensitized state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.52
Minimum - Maximum-1.8136338 - 3.0737443
Average (Standard dev.)0.0048247343 (±0.1273396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34197_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: GluK1-1a captured in the desensitized state additional map

Fileemd_34197_additional_1.map
AnnotationGluK1-1a captured in the desensitized state additional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GluK1-1a captured in the desensitized state half map A

Fileemd_34197_half_map_1.map
AnnotationGluK1-1a captured in the desensitized state half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GluK1-1a captured in the desensitized state half map B

Fileemd_34197_half_map_2.map
AnnotationGluK1-1a captured in the desensitized state half map 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 : GluK1-1a receptor in complex with SYM2081

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

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Supramolecule #1: GluK1-1a receptor in complex with SYM2081

SupramoleculeName: GluK1-1a receptor in complex with SYM2081 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 381 KDa

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Macromolecule #1: Glutamate receptor

MacromoleculeName: Glutamate receptor / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 95.606672 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 R

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

Concentration0.57 mg/mL
BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 60.0 sec. / Average electron dose: 19.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 13750
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5kuf


Details: LBD: 3C32 TMD: 5KUF
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.3.2.0) / Number images used: 5372
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8gpr:
GluK1-1a receptor captured in the desensitized state

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