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- EMDB-23017: GluK2/K5 apo -

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Basic information

Entry
Database: EMDB / ID: EMD-23017
TitleGluK2/K5 apo
Map dataGluK2/K5 apo
Sample
  • Complex: GluK2/K5 apo
    • Protein or peptide: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
    • Protein or peptide: Glutamate receptor ionotropic, kainate 2
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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / 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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / behavioral fear response / neuronal action potential / positive regulation of synaptic transmission / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / bioluminescence / regulation of membrane potential / SNARE binding / excitatory postsynaptic potential / generation of precursor metabolites and energy / synaptic transmission, glutamatergic / establishment of localization in cell / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / cellular response to glucose stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / SH3 domain binding / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / dendrite / ubiquitin protein ligase binding / 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 / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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, GFP / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Green fluorescent protein / Glutamate receptor ionotropic, kainate 2 / Glutamate receptor ionotropic, kainate 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsKhanra N / Brown PMGE / Perozzo AM / Bowie D / Meyerson JM
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 21, 2020-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.358
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.358
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23017.png

Downloads & links

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Map

FileDownload / File: emd_23017.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluK2/K5 apo
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 416 pix.
= 450.528 Å		1.08 Å/pix.
x 416 pix.
= 450.528 Å		1.08 Å/pix.
x 416 pix.
= 450.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.358 / Movie #1: 0.358
Minimum - Maximum-0.43334454 - 0.8805957
Average (Standard dev.)-0.00028282037 (±0.036621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 450.52798 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0831.0831.083
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z450.528450.528450.528
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS416416416
D min/max/mean-0.4330.881-0.000

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Supplemental data

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Sample components

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Entire : GluK2/K5 apo

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

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Supramolecule #1: GluK2/K5 apo

SupramoleculeName: GluK2/K5 apo / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293S GnTI-

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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 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPAELLLLLI VAFANPSCQV LSSLRMAAIL DDQTVCGRGE RLALALAREQ INGIIEVPAK ARVEVDIFE LQRDSQYETT DTMCQILPKG VVSVLGPSSS PASASTVSHI CGEKEIPHIK V GPEETPRL QYLRFASVSL YPSNEDVSLA VSRILKSFNY PSASLICAKA ...String:
MPAELLLLLI VAFANPSCQV LSSLRMAAIL DDQTVCGRGE RLALALAREQ INGIIEVPAK ARVEVDIFE LQRDSQYETT DTMCQILPKG VVSVLGPSSS PASASTVSHI CGEKEIPHIK V GPEETPRL QYLRFASVSL YPSNEDVSLA VSRILKSFNY PSASLICAKA ECLLRLEELV RG FLISKET LSVRMLDDSR DPTPLLKEIR DDKVSTIIID ANASISHLVL RKASELGMTS AFY KYILTT MDFPILHLDG IVEDSSNILG FSMFNTSHPF YPEFVRSLNM SWRENCEAST YPGP ALSAA LMFDAVHVVV SAVRELNRSQ EIGVKPLACT SANIWPHGTS LMNYLRMVEY DGLTG RVEF NSKGQRTNYT LRILEKSRQG HREIGVWYSN RTLAMNATTL DINLSQTLAN KTLVVT TIL ENPYVMRRPN FQALSGNERF EGFCVDMLRE LAELLRFRYR LRLVEDGLYG APEPNGS WT GMVGELINRK ADLAVAAFTI TAEREKVIDF SKPFMTLGIS ILYRVHMGRK PGYFSFLD P FSPAVWLFML LAYLAVSVVL FLAARLSPYE WYNPHPSLRA RPHILENQYT LGNSLWFPV GGFMQQGSEI MPRALSTRIV SGVWWAFTLI IISSYTANLA AFLTVQRMEV PVESADDLAD QTNIEYGTI HAGSTMTFFQ NSRYQTYQRM WNYMQSKQPS VFVKSTEEGI ARVLNSRYAF L LESTMNEY HRRLNCNLTQ IGGLLDTKGY GIGMPLGSPF RDEITLAILQ LQENNRLEIL KR KWWEGGR CPKEEDHRAK GLGMENIGGI FVVLIAGLII AVFVAVMEFI YKSRAEAKRM KGL VPRGSA AAAMVSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD ATYGKLTLKF ICTT GKLPV PWPTLVTTLT YGVQCFSRYP DHMKQHDFFK SAMPEGYVQE RTIFFKDDGN YKTRA EVKF EGDTLVNRIE LKGIDFKEDG NILGHKLEYN YNSHNVYIMA DKQKNGIKVN FKIRHN IED GSVQLADHYQ QNTPIGDGPV LLPDNHYLST QSKLSKDPNE KRDHMVLLEF VTAAGIT LG MDELYKSGLR TETSQVAPA

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Macromolecule #2: Glutamate receptor ionotropic, kainate 2

MacromoleculeName: Glutamate receptor ionotropic, kainate 2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKIISPVLSN LVFSRSIKVL LCLLWIGYSQ GTTHVLRFGG IFEYVESGPM GAEELAFRFA VNTINRNRTL LPNTTLTYDT QKINLYDSFE ASKKACDQLS LGVAAIFGPS HSSSANAVQS ICNALGVPHI QTRWKHQVSD NKDSFYVSLY PDFSSLSRAI LDLVQFFKWK ...String:
MKIISPVLSN LVFSRSIKVL LCLLWIGYSQ GTTHVLRFGG IFEYVESGPM GAEELAFRFA VNTINRNRTL LPNTTLTYDT QKINLYDSFE ASKKACDQLS LGVAAIFGPS HSSSANAVQS ICNALGVPHI QTRWKHQVSD NKDSFYVSLY PDFSSLSRAI LDLVQFFKWK TVTVVYDDST GLIRLQELIK APSRYNLRLK IRQLPADTKD AKPLLKEMKR GKEFHVIFDC SHEMAAGILK QALAMGMMTE YYHYIFTTLD LFALDVEPYR YSGVNMTGFR ILNTENTQVS SIIEKWSMER LQAPPKPDSG LLDGFMTTDA ALMYDAVHVV SVAVQQFPQM TVSSLQCNRH KPWRFGTRFM SLIKEAHWEG LTGRITFNKT NGLRTDFDLD VISLKEEGLE KIGTWDPASG LNMTESQKGK PANITDSLSN RSLIVTTILE EPYVLFKKSD KPLYGNDRFE GYCIDLLREL STILGFTYEI RLVEDGKYGA QDDVNGQWNG MVRELIDHKA DLAVAPLAIT YVREKVIDFS KPFMTLGISI LYRKPNGTNP GVFSFLNPLS PDIWMYVLLA YLGVSVVLFV IARFSPYEWY NPHPSNPDSD VVENNFTLLN SFWFGVGALM QQGSELMPKA LSTRIVGGIW WFFTLIIISS YTANLAAFLT VERMESPIDS ADDLAKQTKI EYGAVEDGAT MTFFKKSKIS TYDKMWAFMS SRRQSVLVKS NEEGIQRVLT SDYAFLMEST TIEFVTQRNC NLTQIGGLID SKGYGVGTPM GSPYRDKITI AILQLQEEGK LHMMKEKWWR GNGCPEEESK EASALGVQNI GGIFIVLAAG LVLSVFVAVG EFLYKSKKNA QLEKRSFCSA MVEELRMSLK CQRRLKHKPQ APVIVKTEEV INMHTFNDRR LPGKETMASG LRSAWSHPQF EKGGGSGGGS GGGSWSHPQF EK

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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

Concentration3.7 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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.23 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90027
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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