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- EMDB-34083: GluK1-1a extracellular domain captured in SYM2081 bound desensiti... -

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Basic information

Entry
Database: EMDB / ID: EMD-34083
TitleGluK1-1a extracellular domain captured in SYM2081 bound desensitized state
Map dataGluK1-1a extracellular domain captured in desensitized state
Sample
  • Complex: Complex of GluK1-1a extracellular domain with SYM2081
    • Protein or peptide: Glutamate receptor
KeywordsKainate receptor / GluK1-1a splice variant / 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: 8.01 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 13, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34083.png

Downloads & links

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Map

FileDownload / File: emd_34083.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluK1-1a extracellular domain captured in 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: 0.55
Minimum - Maximum-1.3355312 - 2.6262696
Average (Standard dev.)0.0046635456 (±0.10914072)
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_34083_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: GluK1-1a extracellular domain captured in desensitized state additional EM...

Fileemd_34083_additional_1.map
AnnotationGluK1-1a extracellular domain captured in desensitized state_additional EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GluK1-1a extracellular domain captured in desensitized state halfmap A...

Fileemd_34083_half_map_1.map
AnnotationGluK1-1a extracellular domain 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 extracellular domain captured in desensitized state halfmap B...

Fileemd_34083_half_map_2.map
AnnotationGluK1-1a extracellular domain 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 extracellular domain with SYM2081

EntireName: Complex of GluK1-1a extracellular domain with SYM2081
Components
  • Complex: Complex of GluK1-1a extracellular domain with SYM2081
    • Protein or peptide: Glutamate receptor

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Supramolecule #1: Complex of GluK1-1a extracellular domain with SYM2081

SupramoleculeName: Complex of GluK1-1a extracellular domain with SYM2081 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 390 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) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1100 / 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

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3c32


Details: Unpublished coordinates for the amino-terminal domain model 3C32 used for ligand binding domain model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5372
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

3c32


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7ysv:
GluK1-1a extracellular domain captured in SYM2081 bound desensitized state

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