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Yorodumi- EMDB-34076: GluK1-1a in nanodisc captured in SYM2081 bound desensitized state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34076 | |||||||||
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Title | GluK1-1a in nanodisc captured in SYM2081 bound desensitized state | |||||||||
Map data | GluK1-1a nanodisc captured in desensitized state | |||||||||
Sample |
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Keywords | Kainate receptor / GluK1-1a splice variant / nanodisc / SYM2081 bound / desensitized state / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information kainate selective glutamate receptor complex / kainate selective glutamate receptor activity / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / presynaptic membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.2 Å | |||||||||
Authors | Dhingra S / Kumar J | |||||||||
Funding support | India, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34076.map.gz | 57.6 MB | EMDB map data format | |
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Header (meta data) | emd-34076-v30.xml emd-34076.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
Images | emd_34076.png | 67.7 KB | ||
Filedesc metadata | emd-34076.cif.gz | 6.3 KB | ||
Others | emd_34076_half_map_1.map.gz emd_34076_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34076 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34076 | HTTPS FTP |
-Validation report
Summary document | emd_34076_validation.pdf.gz | 902.7 KB | Display | EMDB validaton report |
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Full document | emd_34076_full_validation.pdf.gz | 902.2 KB | Display | |
Data in XML | emd_34076_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_34076_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34076 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34076 | HTTPS FTP |
-Related structure data
Related structure data | 7ysjMC 7ysvC 8gprC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34076.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | GluK1-1a nanodisc captured in desensitized state | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.41 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: GluK1-1a nanodisc captured in desensitized state halfmap A
File | emd_34076_half_map_1.map | ||||||||||||
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Annotation | GluK1-1a nanodisc captured in desensitized state_halfmap_A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: GluK1-1a nanodisc captured in desensitized state halfmap B
File | emd_34076_half_map_2.map | ||||||||||||
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Annotation | GluK1-1a nanodisc captured in desensitized state_halfmap_B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of GluK1-1a in lipid nanodisc with SYM2081
Entire | Name: Complex of GluK1-1a in lipid nanodisc with SYM2081 |
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Components |
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-Supramolecule #1: Complex of GluK1-1a in lipid nanodisc with SYM2081
Supramolecule | Name: Complex of GluK1-1a in lipid nanodisc with SYM2081 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: EGFP is covalently conjugated to the C-terminus of GluK1-1a. MSP1E3D1 soybean polar lipid nanodisc used. |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 600 KDa |
-Macromolecule #1: Glutamate receptor
Macromolecule | Name: Glutamate receptor / type: protein_or_peptide / ID: 1 Details: L838-S843 correspond to Thrombin recognition site, A844-A847 correspond to Ala linker, V848-S1090 correspond to enhanced green fluorescent protein (EGFP), H1091-H1098 correspond to Octa-His affinity tag. Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 124.527125 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 RGSAAAAVSK GEELFTGVVP ILVELDGDVN GHKFSVSGEG EGDATYGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKQHD FFKSAMPEGY VQERTIFFKD DGNYKTRAEV K FEGDTLVN RIELKGIDFK EDGNILGHKL EYNYNSHNVY IMADKQKNGI KVNFKIRHNI EDGSVQLADH YQQNTPIGDG PV LLPDNHY LSTQSKLSKD PNEKRDHMVL LEFVTAAGIT LGMDELYKSG LRSHHHHHHH H UniProtKB: Glutamate receptor |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.87 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 12.0 sec. / Average electron dose: 40.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: Unpublished coordinates for the amino-terminal domain model 3C32 used for ligand binding domain model 5KUF used for the trans-membrane domain model |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24531 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |