[English] 日本語
Yorodumi
- EMDB-23015: GluK2/K5 with L-Glu -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23015
TitleGluK2/K5 with L-Glu
Map dataGluK2/K5 with L-Glu (full-length map)
Sample
  • Complex: GluK2/K5 with L-Glu
    • Protein or peptide: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2
KeywordsKainate receptor / ionotropic glutamate receptor / membrane protein / ligand-gated ion channel / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / 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 ...regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / 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 / bioluminescence / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / generation of precursor metabolites and energy / synaptic transmission, glutamatergic / PDZ domain binding / establishment of localization in cell / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / cellular response to glucose stimulus / postsynaptic density membrane / terminal bouton / SH3 domain binding / 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 / endoplasmic reticulum / identical protein binding / membrane / plasma membrane
Similarity search - Function
Green fluorescent protein, GFP / 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 / : / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein ...Green fluorescent protein, GFP / 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 / : / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Green fluorescent protein / Glutamate receptor ionotropic, kainate 2 / Glutamate receptor ionotropic, kainate 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsKhanra N / Brown PMGE
CitationJournal: Elife / Year: 2021
Title: Architecture and structural dynamics of the heteromeric GluK2/K5 kainate receptor.
Authors: Nandish Khanra / Patricia Mge Brown / Amanda M Perozzo / Derek Bowie / Joel R Meyerson /
Abstract: Kainate receptors (KARs) are L-glutamate-gated ion channels that regulate synaptic transmission and modulate neuronal circuits. KARs have strict assembly rules and primarily function as heteromeric ...Kainate receptors (KARs) are L-glutamate-gated ion channels that regulate synaptic transmission and modulate neuronal circuits. KARs have strict assembly rules and primarily function as heteromeric receptors in the brain. A longstanding question is how KAR heteromer subunits organize and coordinate together to fulfill their signature physiological roles. Here we report structures of the GluK2/GluK5 heteromer in apo, antagonist-bound, and desensitized states. The receptor assembles with two copies of each subunit, ligand binding domains arranged as two heterodimers and GluK5 subunits proximal to the channel. Strikingly, during desensitization, GluK2, but not GluK5, subunits undergo major structural rearrangements to facilitate channel closure. We show how the large conformational differences between antagonist-bound and desensitized states are mediated by the linkers connecting the pore helices to the ligand binding domains. This work presents the first KAR heteromer structure, reveals how its subunits are organized, and resolves how the heteromer can accommodate functionally distinct closed channel structures.
History
DepositionNov 20, 2020-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.387
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.387
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ks3
  • Surface level: 0.387
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23015.png

Downloads & links

-
Map

FileDownload / File: emd_23015.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluK2/K5 with L-Glu (full-length map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 350.72 Å		1.1 Å/pix.
x 320 pix.
= 350.72 Å		1.1 Å/pix.
x 320 pix.
= 350.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.387 / Movie #1: 0.387
Minimum - Maximum-0.7595134 - 1.429554
Average (Standard dev.)0.0026472716 (±0.05599474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 350.71997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0961.0961.096
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z350.720350.720350.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.7601.4300.003

-
Supplemental data

-
Additional map: GluK2/K5 with L-Glu (ATD map)

Fileemd_23015_additional_1.map
AnnotationGluK2/K5 with L-Glu (ATD map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: GluK2/K5 with L-Glu (LBD-TMD map)

Fileemd_23015_additional_2.map
AnnotationGluK2/K5 with L-Glu (LBD-TMD map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GluK2/K5 with L-Glu

EntireName: GluK2/K5 with L-Glu
Components
  • Complex: GluK2/K5 with L-Glu
    • Protein or peptide: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2

-
Supramolecule #1: GluK2/K5 with L-Glu

SupramoleculeName: GluK2/K5 with L-Glu / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

-
Macromolecule #1: Glutamate receptor ionotropic, kainate 5,Green fluorescent protei...

MacromoleculeName: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 123.676812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPAELLLLLI VAFANPSCQV LSSLRMAAIL DDQTVCGRGE RLALALAREQ INGIIEVPAK ARVEVDIFEL QRDSQYETTD TMCQILPKG VVSVLGPSSS PASASTVSHI CGEKEIPHIK VGPEETPRLQ YLRFASVSLY PSNEDVSLAV SRILKSFNYP S ASLICAKA ...String:
MPAELLLLLI VAFANPSCQV LSSLRMAAIL DDQTVCGRGE RLALALAREQ INGIIEVPAK ARVEVDIFEL QRDSQYETTD TMCQILPKG VVSVLGPSSS PASASTVSHI CGEKEIPHIK VGPEETPRLQ YLRFASVSLY PSNEDVSLAV SRILKSFNYP S ASLICAKA ECLLRLEELV RGFLISKETL SVRMLDDSRD PTPLLKEIRD DKVSTIIIDA NASISHLVLR KASELGMTSA FY KYILTTM DFPILHLDGI VEDSSNILGF SMFNTSHPFY PEFVRSLNMS WRENCEASTY PGPALSAALM FDAVHVVVSA VRE LNRSQE IGVKPLACTS ANIWPHGTSL MNYLRMVEYD GLTGRVEFNS KGQRTNYTLR ILEKSRQGHR EIGVWYSNRT LAMN ATTLD INLSQTLANK TLVVTTILEN PYVMRRPNFQ ALSGNERFEG FCVDMLRELA ELLRFRYRLR LVEDGLYGAP EPNGS WTGM VGELINRKAD LAVAAFTITA EREKVIDFSK PFMTLGISIL YRVHMGRKPG YFSFLDPFSP AVWLFMLLAY LAVSVV LFL AARLSPYEWY NPHPSLRARP HILENQYTLG NSLWFPVGGF MQQGSEIMPR ALSTRIVSGV WWAFTLIIIS SYTANLA AF LTVQRMEVPV ESADDLADQT NIEYGTIHAG STMTFFQNSR YQTYQRMWNY MQSKQPSVFV KSTEEGIARV LNSRYAFL L ESTMNEYHRR LNCNLTQIGG LLDTKGYGIG MPLGSPFRDE ITLAILQLQE NNRLEILKRK WWEGGRCPKE EDHRAKGLG MENIGGIFVV LIAGLIIAVF VAVMEFIYKS RAEAKRMKGL VPRGSAAAAM VSKGEELFTG VVPILVELDG DVNGHKFSVS GEGEGDATY GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK QHDFFKSAMP EGYVQERTIF FKDDGNYKTR A EVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNYNSH NVYIMADKQK NGIKVNFKIR HNIEDGSVQL ADHYQQNTPI GD GPVLLPD NHYLSTQSKL SKDPNEKRDH MVLLEFVTAA GITLGMDELY KSGLRTETSQ VAPA

UniProtKB: Glutamate receptor ionotropic, kainate 5, Green fluorescent protein

-
Macromolecule #2: Glutamate receptor ionotropic, kainate 2

MacromoleculeName: Glutamate receptor ionotropic, kainate 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 105.981617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKIISPVLSN LVFSRSIKVL LCLLWIGYSQ GTTHVLRFGG IFEYVESGPM GAEELAFRFA VNTINRNRTL LPNTTLTYDT QKINLYDSF EASKKACDQL SLGVAAIFGP SHSSSANAVQ SICNALGVPH IQTRWKHQVS DNKDSFYVSL YPDFSSLSRA I LDLVQFFK ...String:
MKIISPVLSN LVFSRSIKVL LCLLWIGYSQ GTTHVLRFGG IFEYVESGPM GAEELAFRFA VNTINRNRTL LPNTTLTYDT QKINLYDSF EASKKACDQL SLGVAAIFGP SHSSSANAVQ SICNALGVPH IQTRWKHQVS DNKDSFYVSL YPDFSSLSRA I LDLVQFFK WKTVTVVYDD STGLIRLQEL IKAPSRYNLR LKIRQLPADT KDAKPLLKEM KRGKEFHVIF DCSHEMAAGI LK QALAMGM MTEYYHYIFT TLDLFALDVE PYRYSGVNMT GFRILNTENT QVSSIIEKWS MERLQAPPKP DSGLLDGFMT TDA ALMYDA VHVVSVAVQQ FPQMTVSSLQ CNRHKPWRFG TRFMSLIKEA HWEGLTGRIT FNKTNGLRTD FDLDVISLKE EGLE KIGTW DPASGLNMTE SQKGKPANIT DSLSNRSLIV TTILEEPYVL FKKSDKPLYG NDRFEGYCID LLRELSTILG FTYEI RLVE DGKYGAQDDV NGQWNGMVRE LIDHKADLAV APLAITYVRE KVIDFSKPFM TLGISILYRK PNGTNPGVFS FLNPLS PDI WMYVLLAYLG VSVVLFVIAR FSPYEWYNPH PSNPDSDVVE NNFTLLNSFW FGVGALMQQG SELMPKALST RIVGGIW WF FTLIIISSYT ANLAAFLTVE RMESPIDSAD DLAKQTKIEY GAVEDGATMT FFKKSKISTY DKMWAFMSSR RQSVLVKS N EEGIQRVLTS DYAFLMESTT IEFVTQRNCN LTQIGGLIDS KGYGVGTPMG SPYRDKITIA ILQLQEEGKL HMMKEKWWR GNGCPEEESK EASALGVQNI GGIFIVLAAG LVLSVFVAVG EFLYKSKKNA QLEKRSFCSA MVEELRMSLK CQRRLKHKPQ APVIVKTEE VINMHTFNDR RLPGKETMAS GLRSAWSHPQ FEKGGGSGGG SGGGSWSHPQ FEK

UniProtKB: Glutamate receptor ionotropic, kainate 2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.7 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
20.0 mMTris
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details1 mM L-Glu

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Number of particles for ATD map: 241849 Number of particles for LBD-TMD map: 140028
Number images used: 573403
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more