[English] 日本語
Yorodumi
- EMDB-34083: GluK1-1a extracellular domain captured in SYM2081 bound desensiti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34083
TitleGluK1-1a extracellular domain captured in SYM2081 bound desensitized state
Map dataGluK1-1a extracellular domain captured in desensitized state
Sample
  • Complex: Complex of GluK1-1a extracellular domain with SYM2081
    • Protein or peptide: Glutamate receptor
KeywordsKainate 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
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.01 Å
AuthorsDhingra S / Kumar J
Funding support India, 1 items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2020/003971 India
CitationJournal: 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
DepositionAug 13, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34083.png

Downloads & links

-
Map

FileDownload / File: emd_34083.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluK1-1a extracellular domain captured in desensitized state
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-1.3355312 - 2.6262696
Average (Standard dev.)0.0046635456 (±0.10914072)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34083_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: GluK1-1a extracellular domain captured in desensitized state additional EM...

Fileemd_34083_additional_1.map
AnnotationGluK1-1a extracellular domain captured in desensitized state_additional EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: GluK1-1a extracellular domain captured in desensitized state halfmap A...

Fileemd_34083_half_map_1.map
AnnotationGluK1-1a extracellular domain captured in desensitized state halfmap_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: GluK1-1a extracellular domain captured in desensitized state halfmap B...

Fileemd_34083_half_map_2.map
AnnotationGluK1-1a extracellular domain captured in desensitized state halfmap_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of GluK1-1a extracellular domain with SYM2081

EntireName: Complex of GluK1-1a extracellular domain with SYM2081
Components
  • Complex: Complex of GluK1-1a extracellular domain with SYM2081
    • Protein or peptide: Glutamate receptor

-
Supramolecule #1: Complex of GluK1-1a extracellular domain with SYM2081

SupramoleculeName: Complex of GluK1-1a extracellular domain with SYM2081 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 390 KDa

-
Macromolecule #1: Glutamate receptor

MacromoleculeName: Glutamate receptor / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 95.606672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.57 mg/mL
BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3c32


Details: Unpublished coordinates for the amino-terminal domain model 3C32 used for ligand binding domain model
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5372

-
Atomic model buiding 1

Initial modelPDB ID:

3c32


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7ysv:
GluK1-1a extracellular domain captured in SYM2081 bound desensitized state

+
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