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- EMDB-0774: Rat GluD1 receptor(compact conformation) in complex with 7-CKA an... -

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Basic information

Entry
Database: EMDB / ID: EMD-0774
TitleRat GluD1 receptor(compact conformation) in complex with 7-CKA and Calcium ions
Map datafinal refined map
Sample
  • Complex: GluD1
    • Protein or peptide: Glutamate receptor ionotropic, delta-1
Keywordscomplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


glutamate receptor activity / regulation of postsynapse organization / regulation of postsynaptic membrane neurotransmitter receptor levels / social behavior / GABA-ergic synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / postsynaptic membrane ...glutamate receptor activity / regulation of postsynapse organization / regulation of postsynaptic membrane neurotransmitter receptor levels / social behavior / GABA-ergic synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / postsynaptic membrane / glutamatergic synapse / identical protein binding / 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, delta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsBurada AP / Kumar J
Funding support India, 1 items
OrganizationGrant numberCountry
Wellcome TrustIA/I/13/2/5010023 India
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structures of the ionotropic glutamate receptor GluD1 reveal a non-swapped architecture.
Authors: Ananth Prasad Burada / Rajesh Vinnakota / Janesh Kumar /
Abstract: Ionotropic orphan delta (GluD) receptors are not gated by glutamate or any other endogenous ligand but are grouped with ionotropic glutamate receptors (iGluRs) based on sequence similarity. GluD1 ...Ionotropic orphan delta (GluD) receptors are not gated by glutamate or any other endogenous ligand but are grouped with ionotropic glutamate receptors (iGluRs) based on sequence similarity. GluD1 receptors play critical roles in synaptogenesis and synapse maintenance and have been implicated in neuronal disorders, including schizophrenia, cognitive deficits, and cerebral ataxia. Here we report cryo-EM structures of the rat GluD1 receptor complexed with calcium and the ligand 7-chlorokynurenic acid (7-CKA), elucidating molecular architecture and principles of receptor assembly. The structures reveal a non-swapped architecture at the interface of the extracellular amino-terminal domain (ATD) and the ligand-binding domain (LBD). This finding is in contrast with structures of other families of iGluRs, where the dimer partners between the ATD and LBD layers are swapped. Our results demonstrate that principles of architecture and symmetry are not conserved between delta receptors and other iGluRs and provide a molecular blueprint for understanding the functions of the 'orphan' class of iGluRs.
History
DepositionAug 26, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.325
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.325
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kss
  • Surface level: 0.325
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0774.png

Downloads & links

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Map

FileDownload / File: emd_0774.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal refined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 426.8 Å		1.07 Å/pix.
x 400 pix.
= 426.8 Å		1.07 Å/pix.
x 400 pix.
= 426.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.325 / Movie #1: 0.325
Minimum - Maximum-1.0635847 - 1.8846725
Average (Standard dev.)0.0010700548 (±0.072161205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 426.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z426.800426.800426.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.0641.8850.001

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Supplemental data

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Half map: half map A

Fileemd_0774_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_0774_half_map_2.map
Annotationhalf 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 : GluD1

EntireName: GluD1
Components
  • Complex: GluD1
    • Protein or peptide: Glutamate receptor ionotropic, delta-1

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Supramolecule #1: GluD1

SupramoleculeName: GluD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Recombinantly expressed protein
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 388 KDa

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Macromolecule #1: Glutamate receptor ionotropic, delta-1

MacromoleculeName: Glutamate receptor ionotropic, delta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 95.718039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DSIIHIGAIF EENAAKDDRV FQLAVSDLSL NDDILQSEKI TYSIKVIEAN NPFQAVQEAC DLMTQGILAL VTSTGCASAN ALQSLTDAM HIPHLFVQRN PGGSPRTACH LNPSPDGEAY TLASRPPVRL NDVMLRLVTE LRWQKFVMFY DSEYDIRGLQ S FLDQASRL ...String:
DSIIHIGAIF EENAAKDDRV FQLAVSDLSL NDDILQSEKI TYSIKVIEAN NPFQAVQEAC DLMTQGILAL VTSTGCASAN ALQSLTDAM HIPHLFVQRN PGGSPRTACH LNPSPDGEAY TLASRPPVRL NDVMLRLVTE LRWQKFVMFY DSEYDIRGLQ S FLDQASRL GLDVSLQKVD KNISHVFTSL FTTMKTEELN RYRDTLRRAI LLLSPQGAHS FINEAVETNL ASKDSHWVFV NE EISDPEI LDLVHSALGR MTVVRQIFPS AKDNQKCMRN NHRISSLLCD PQEGYLQMLQ ISNLYLYDSV LMLANAFHRK LED RKWHSM ASLNCIRKST KPWNGGRSML DTIKKGHITG LTGVMEFRED SSNPYVQFEI LGTTYSETFG KDMRKLATWD SEKG LNGSL QERPMGSRLQ GLTLKVVTVL EEPFVMVAEN ILGQPKRYKG FSIDVLDALA KALGFKYEIY QAPDGRYGHQ LHNTS WNGM IGELISKRAD LAISAITITP ERESVVDFSK RYMDYSVGIL IKKPEEKISI FSLFAPFDFA VWACIAAAIP VVGVLI FVL NRIQAVRSQS ATQPRPSASA TLHSAIWIVY GAFVQQGGES SVNSVAMRIV MGSWWLFTLI VCSSYTANLA AFLTVSR MD SPVRTFQDLS KQLEMSYGTV RDSAVYEYFR AKGTNPLEQD STFAELWRTI SKNGGADNCV SNPSEGIRKA KKGNYAFL W DVAVVEYAAL TDDDCSVTVI GNSISSKGYG IALQHGSPYR DLFSQRILEL QDTGDLDVLK QKWWPHTGRC DLTSHSSAQ TDGKSLKLHS FAGVFCILAI GLLLACLVAA LELWWNSNRC HQETPKEDKE VGLVPR

UniProtKB: Glutamate receptor ionotropic, delta-1

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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

Concentration0.9 mg/mL
BufferpH: 8 / Details: 20mM Tris, 150mM NaCl, 0.75mM DDM, 0.025mM CHS
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 0-40 / Number real images: 4120 / Average exposure time: 6.0 sec. / Average electron dose: 40.38 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2000
Details: Particles were picked manually, which were used as reference for autopicking.
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2.9.0) / Number images used: 13422
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v2.9.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v2.9.0) / Software - details: local refinement
Final 3D classificationNumber classes: 7 / Avg.num./class: 11000 / Software - Name: cryoSPARC (ver. v2.9.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6kss:
Rat GluD1 receptor(compact conformation) in complex with 7-CKA and Calcium ions

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