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Yorodumi- EMDB-36900: Cryo-EM structure of niacin bound human hydroxy-carboxylic acid r... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36900 | |||||||||
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Title | Cryo-EM structure of niacin bound human hydroxy-carboxylic acid receptor 2 (Local refinement) | |||||||||
Map data | sharpening map | |||||||||
Sample |
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Keywords | GPCR / G-Protein / MEMBRANE PROTEIN / signaling | |||||||||
Function / homology | Function and homology information nicotinic acid receptor activity / Hydroxycarboxylic acid-binding receptors / neutrophil apoptotic process / Class A/1 (Rhodopsin-like receptors) / positive regulation of neutrophil apoptotic process / positive regulation of adiponectin secretion / negative regulation of lipid catabolic process / cell junction / G alpha (i) signalling events / G protein-coupled receptor signaling pathway / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.43 Å | |||||||||
Authors | Park JH / Ishimoto N / Park SY | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2 Authors: Park JH / Kawakami K / Ishimoto N / Ikuta T / Ohki M / Ekimoto T / Ikeguchi M / Lee DS / Lee YH / Tame JRH / Inoue A / Park SY | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36900.map.gz | 28.8 MB | EMDB map data format | |
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Header (meta data) | emd-36900-v30.xml emd-36900.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36900_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_36900.png | 27.4 KB | ||
Masks | emd_36900_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-36900.cif.gz | 5.9 KB | ||
Others | emd_36900_additional_1.map.gz emd_36900_half_map_1.map.gz emd_36900_half_map_2.map.gz | 15.3 MB 28.3 MB 28.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36900 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36900 | HTTPS FTP |
-Related structure data
Related structure data | 8k5bMC 8k5cC 8k5dC 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_36900.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpening map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_36900_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: map
File | emd_36900_additional_1.map | ||||||||||||
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Annotation | map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_36900_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_36900_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Niacin bound human hydroxy-carboxylic acid receptor 2
Entire | Name: Niacin bound human hydroxy-carboxylic acid receptor 2 |
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Components |
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-Supramolecule #1: Niacin bound human hydroxy-carboxylic acid receptor 2
Supramolecule | Name: Niacin bound human hydroxy-carboxylic acid receptor 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Human Hydroxycarboxylic acid receptor 2
Macromolecule | Name: Human Hydroxycarboxylic acid receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54.320297 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GPGAPADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKV KEAQAAAEQL KTTRNAYIQK YLEFMNRHHL QDHFLEIDKK NCCVFRDDFI VKVLPPVLGL EFIFGLLGNG L ALWIFCFH ...String: GPGAPADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKV KEAQAAAEQL KTTRNAYIQK YLEFMNRHHL QDHFLEIDKK NCCVFRDDFI VKVLPPVLGL EFIFGLLGNG L ALWIFCFH LKSWKSSRIF LFNLAVADFL LIICLPFLMD NYVRRWDWKF GDIPCRLMLF MLAMNRQGSI IFLTVVAVDR YF RVVHPHH ALNKISNRTA AIISCLLWGI TIGLTVHLLK KKMPIQNGGA NLCSSFSICH TFQWHEAMFL LEFFLPLGII LFC SARIIW SLRQRQMDRH AKIKRAITFI MVVAIVFVIC FLPSVVVRIR IFWLLHTSGT QNCEVYRSVD LAFFITLSFT YMNS MLDPV VYYFSSPSFP NFFSTLINRC LQRKMTGEPD NNRSTSVELT GDPNKTRGAP EALMANSGEP WSPSYLGPTS P UniProtKB: Hydroxycarboxylic acid receptor 2 |
-Macromolecule #2: NICOTINIC ACID
Macromolecule | Name: NICOTINIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: NIO |
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Molecular weight | Theoretical: 123.109 Da |
Chemical component information | ChemComp-NIO: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.1 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8k5b: |