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- EMDB-29926: Domoate-bound GluK2 kainate receptor in partially-open conformation 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-29926
TitleDomoate-bound GluK2 kainate receptor in partially-open conformation 1
Map dataDomoate-bound GluK2 kainate receptor in partially-open conformation 1
Sample
  • Complex: Homotetrameric GluK2 bound with domoate state 1
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID
Keywordsion channel / glutamate kainate receptor 2 / homotetramer / MEMBRANE PROTEIN / partial agonist / gating mechanism
Function / homology
Function and homology information


mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / regulation of JNK cascade / receptor clustering / modulation of excitatory postsynaptic potential / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / behavioral fear response / positive regulation of synaptic transmission / neuronal action potential / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / presynaptic modulation of chemical synaptic transmission / SNARE binding / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / neuron apoptotic process / chemical synaptic transmission / perikaryon / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / synapse / dendrite / ubiquitin protein ligase binding / glutamatergic synapse / identical protein binding / membrane / plasma 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
Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsBogdanovic N / Tajima N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM147266-01 United States
CitationJournal: To Be Published
Title: Structural basis for kainate receptor activation by a partial agonist
Authors: Bogdanovic N / Tajima N
History
DepositionMar 1, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29926.png

Downloads & links

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Map

FileDownload / File: emd_29926.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDomoate-bound GluK2 kainate receptor in partially-open conformation 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0145
Minimum - Maximum-0.008144713 - 0.042658657
Average (Standard dev.)0.00013984235 (±0.001441406)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 445.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29926_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map

Fileemd_29926_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_29926_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_29926_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homotetrameric GluK2 bound with domoate state 1

EntireName: Homotetrameric GluK2 bound with domoate state 1
Components
  • Complex: Homotetrameric GluK2 bound with domoate state 1
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID

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Supramolecule #1: Homotetrameric GluK2 bound with domoate state 1

SupramoleculeName: Homotetrameric GluK2 bound with domoate state 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Tetramer isolated and dyalised extensively. The domoate was applied prior to grid freezing.
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Glutamate receptor ionotropic, kainate 2

MacromoleculeName: Glutamate receptor ionotropic, kainate 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 98.883469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HVLRFGGIFE YVESGPMGAE ELAFRFAVNT INRNRTLLPN TTLTYDTQKI NLYDSFEASK KACDQLSLGV AAIFGPSHSS SANAVQSIC NALGVPHIQT RWKHQVSDNK DSFYVSLYPD FSSLSRAILD LVQFFKWKTV TVVYDDSTGL IRLQELIKAP S RYNLRLKI ...String:
HVLRFGGIFE YVESGPMGAE ELAFRFAVNT INRNRTLLPN TTLTYDTQKI NLYDSFEASK KACDQLSLGV AAIFGPSHSS SANAVQSIC NALGVPHIQT RWKHQVSDNK DSFYVSLYPD FSSLSRAILD LVQFFKWKTV TVVYDDSTGL IRLQELIKAP S RYNLRLKI RQLPADTKDA KPLLKEMKRG KEFHVIFDCS HEMAAGILKQ ALAMGMMTEY YHYIFTTLDL FALDVEPYRY SG VNMTGFR ILNTENTQVS SIIEKWSMER LQAPPKPDSG LLDGFMTTDA ALMYDAVHVV SVAVQQFPQM TVSSLQCNRH KPW RFGTRF MSLIKEAHWE GLTGRITFNK TNGLRTDFDL DVISLKEEGL EKIGTWDPAS GLNMTESQKG KPANITDSLS NRSL IVTTI LEEPYVLFKK SDKPLYGNDR FEGYCIDLLR ELSTILGFTY EIRLVEDGKY GAQDDVNGQW NGMVRELIDH KADLA VAPL AITYVREKVI DFSKPFMTLG ISILYRKPNG TNPGVFSFLN PLSPDIWMYV LLAYLGVSVV LFVIARFSPY EWYNPH PSN PDSDVVENNF TLLNSFWFGV GALMQQGSEL MPKALSTRIV GGIWWFFTLI IISSYTANLA AFLTVERMES PIDSADD LA KQTKIEYGAV EDGATMTFFK KSKISTYDKM WAFMSSRRQS VLVKSNEEGI QRVLTSDYAF LMESTTIEFV TQRNCNLT Q IGGLIDSKGY GVGTPMGSPY RDKITIAILQ LQEEGKLHMM KEKWWRGNGC PEEESKEASA LGVQNIGGIF IVLAAGLVL SVFVAVGEFL YKSKKNAQLE KRSFCSAMVE ELRMSLKCQR RLKHKPQAPV IVKTEEVINM HTFNDRRLPG KETMA

UniProtKB: Glutamate receptor ionotropic, kainate 2

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIE...

MacromoleculeName: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID
type: ligand / ID: 7 / Number of copies: 3 / Formula: DOQ
Molecular weightTheoretical: 311.33 Da
Chemical component information

ChemComp-DOQ:
(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID / neurotoxin*YM

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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

Concentration3.5 mg/mL
BufferpH: 8 / Component - Concentration: 150.0 mmol / Component - Formula: NaCl / Component - Name: sodium chloride / Details: 50 mM Tris/HCl 150 mM NaCl 1mM DDM pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was isolated from SEC and concentrated. Monodispersity of the final sample determined by the analytical HPLC, S200i column.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12486 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2481151
Details: Initially picked particles that are later classified in several rounds of 2D and 3D classifications. The number of final classes for this dataset is 4 of which this state represents "class ...Details: Initially picked particles that are later classified in several rounds of 2D and 3D classifications. The number of final classes for this dataset is 4 of which this state represents "class 1" and contains 39636 as the final number of particles.
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5kuf

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Software - details: beta / Number images used: 39636
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0) / Software - details: beta
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 4.0) / Software - details: beta
Final 3D classificationNumber classes: 5 / Avg.num./class: 60000 / Software - Name: RELION (ver. 4.0) / Software - details: beta
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 30 / Target criteria: 0.85
Output model

PDB-8gc2:
Domoate-bound GluK2 kainate receptor in partially-open conformation 1

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