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Yorodumi- EMDB-34083: GluK1-1a extracellular domain captured in SYM2081 bound desensiti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34083 | |||||||||
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Title | GluK1-1a extracellular domain captured in SYM2081 bound desensitized state | |||||||||
Map data | GluK1-1a extracellular domain captured in desensitized state | |||||||||
Sample |
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Keywords | Kainate receptor / GluK1-1a splice variant / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information ligand-gated monoatomic ion channel activity / signaling receptor activity / postsynaptic membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.01 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_34083.map.gz | 32.6 MB | EMDB map data format | |
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Header (meta data) | emd-34083-v30.xml emd-34083.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_34083.png | 51.3 KB | ||
Masks | emd_34083_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-34083.cif.gz | 6 KB | ||
Others | emd_34083_additional_1.map.gz emd_34083_half_map_1.map.gz emd_34083_half_map_2.map.gz | 57.6 MB 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34083 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34083 | HTTPS FTP |
-Validation report
Summary document | emd_34083_validation.pdf.gz | 947 KB | Display | EMDB validaton report |
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Full document | emd_34083_full_validation.pdf.gz | 946.5 KB | Display | |
Data in XML | emd_34083_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_34083_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34083 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34083 | HTTPS FTP |
-Related structure data
Related structure data | 7ysvMC 7ysjC 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_34083.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | GluK1-1a extracellular domain captured in desensitized state | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34083_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: GluK1-1a extracellular domain captured in desensitized state additional EM...
File | emd_34083_additional_1.map | ||||||||||||
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Annotation | GluK1-1a extracellular domain captured in desensitized state_additional EM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: GluK1-1a extracellular domain captured in desensitized state halfmap A...
File | emd_34083_half_map_1.map | ||||||||||||
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Annotation | GluK1-1a extracellular domain captured in desensitized state halfmap_A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: GluK1-1a extracellular domain captured in desensitized state halfmap B...
File | emd_34083_half_map_2.map | ||||||||||||
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Annotation | GluK1-1a extracellular domain captured in desensitized state halfmap_B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of GluK1-1a extracellular domain with SYM2081
Entire | Name: Complex of GluK1-1a extracellular domain with SYM2081 |
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Components |
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-Supramolecule #1: Complex of GluK1-1a extracellular domain with SYM2081
Supramolecule | Name: Complex of GluK1-1a extracellular domain with SYM2081 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 390 KDa |
-Macromolecule #1: Glutamate receptor
Macromolecule | Name: Glutamate receptor / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 95.606672 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 R UniProtKB: Glutamate receptor |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.57 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1100 / Average exposure time: 60.0 sec. / Average electron dose: 19.5 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 |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5372 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |